rs894189

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001039213.4(CEACAM16):c.114G>A(p.Thr38Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 1,613,668 control chromosomes in the GnomAD database, including 6,038 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1622 hom., cov: 32)

Exomes 𝑓: 0.065 ( 4416 hom. )

Consequence

CEACAM16
NM_001039213.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -4.62

Publications

6 publications found

Variant links:

Genes affected

CEACAM16 (HGNC:31948): (CEA cell adhesion molecule 16, tectorial membrane component) The protein encoded by this gene is a secreted glycoprotein that in mouse interacts with tectorial membrane proteins in the inner ear. The encoded adhesion protein is found in cochlear outer hair cells and appears to be important for proper hearing over an extended frequency range. Defects in this gene likely are a cause of non-syndromic autosomal dominant hearing loss. [provided by RefSeq, May 2012]

CEACAM16 links:

CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)

CEACAM16-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 19-44703425-G-A is Benign according to our data. Variant chr19-44703425-G-A is described in ClinVar as Benign. ClinVar VariationId is 226502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.62 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM16	NM_001039213.4 link	c.114G>A	p.Thr38Thr	synonymous_variant	Exon 3 of 7	ENST00000587331.7	NP_001034302.2	Q2WEN9
CEACAM16	XM_017026795.2 link	c.114G>A	p.Thr38Thr	synonymous_variant	Exon 2 of 5		XP_016882284.1
CEACAM16-AS1	NR_186815.1 link	n.348-4248C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM16	ENST00000587331.7 link	c.114G>A	p.Thr38Thr	synonymous_variant	Exon 3 of 7	1	NM_001039213.4	ENSP00000466561.1		Q2WEN9

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17918

AN:

152092

Hom.:

1612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.0628

Gnomad EAS

AF:

0.0501

Gnomad SAS

AF:

0.0972

Gnomad FIN

AF:

0.0547

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0516

Gnomad OTH

AF:

0.111

GnomAD2 exomes

AF:

0.0913

AC:

22708

AN:

248662

AF XY:

0.0855

show subpopulations

Gnomad AFR exome

AF:

0.252

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.0607

Gnomad EAS exome

AF:

0.0430

Gnomad FIN exome

AF:

0.0604

Gnomad NFE exome

AF:

0.0548

Gnomad OTH exome

AF:

0.0860

GnomAD4 exome

AF:

0.0653

AC:

95370

AN:

1461458

Hom.:

4416

Cov.:

AF XY:

0.0647

AC XY:

47012

AN XY:

727032

show subpopulations

African (AFR)

AF:

0.251

AC:

8393

AN:

33478

American (AMR)

AF:

0.191

AC:

8549

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.0597

AC:

1561

AN:

26134

East Asian (EAS)

AF:

0.0484

AC:

1921

AN:

39700

South Asian (SAS)

AF:

0.0897

AC:

7735

AN:

86254

European-Finnish (FIN)

AF:

0.0605

AC:

3218

AN:

53200

Middle Eastern (MID)

AF:

0.0757

AC:

436

AN:

5756

European-Non Finnish (NFE)

AF:

0.0530

AC:

58950

AN:

1111862

Other (OTH)

AF:

0.0763

AC:

4607

AN:

60362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

5343

10686

16028

21371

26714

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2452

4904

7356

9808

12260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.118

AC:

17944

AN:

152210

Hom.:

1622

Cov.:

AF XY:

0.118

AC XY:

8794

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.243

AC:

10088

AN:

41502

American (AMR)

AF:

0.167

AC:

2551

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0628

AC:

218

AN:

3470

East Asian (EAS)

AF:

0.0498

AC:

258

AN:

5180

South Asian (SAS)

AF:

0.0964

AC:

465

AN:

4822

European-Finnish (FIN)

AF:

0.0547

AC:

581

AN:

10616

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0516

AC:

3508

AN:

68018

Other (OTH)

AF:

0.110

AC:

232

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

765

1530

2295

3060

3825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0822

Hom.:

1304

Bravo

AF:

0.134

Asia WGS

AF:

0.0860

AC:

297

AN:

3478

EpiCase

AF:

0.0544

EpiControl

AF:

0.0574

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Aug 03, 2017

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 24, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Thr38Thr in exon 3 of CEACAM16: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 22.9% (951/4144) o f African American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs894189). -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.016

(source)

DANN

Benign

0.67

PhyloP100

-4.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over