rs143934888

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001039213.4(CEACAM16):c.1268-13A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 1,611,874 control chromosomes in the GnomAD database, including 1,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.036 ( 135 hom., cov: 33)

Exomes 𝑓: 0.045 ( 1660 hom. )

Consequence

CEACAM16
NM_001039213.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.60

Publications

2 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 19-44710483-A-G is Benign according to our data. Variant chr19-44710483-A-G is described in ClinVar as Benign. ClinVar VariationId is 226504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM16	NM_001039213.4 link	c.1268-13A>G		intron_variant	Intron 6 of 6	ENST00000587331.7	NP_001034302.2	Q2WEN9
CEACAM16-AS1	NR_186815.1 link	n.348-11306T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM16	ENST00000587331.7 link	c.1268-13A>G		intron_variant	Intron 6 of 6	1	NM_001039213.4	ENSP00000466561.1		Q2WEN9

Frequencies

GnomAD3 genomes

AF:

0.0363

AC:

5514

AN:

152092

Hom.:

135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00850

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0279

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0472

Gnomad FIN

AF:

0.0757

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0502

Gnomad OTH

AF:

0.0383

GnomAD2 exomes

AF:

0.0418

AC:

10357

AN:

247654

AF XY:

0.0436

show subpopulations

Gnomad AFR exome

AF:

0.00725

Gnomad AMR exome

AF:

0.0237

Gnomad ASJ exome

AF:

0.0457

Gnomad EAS exome

AF:

0.000280

Gnomad FIN exome

AF:

0.0793

Gnomad NFE exome

AF:

0.0499

Gnomad OTH exome

AF:

0.0524

GnomAD4 exome

AF:

0.0455

AC:

66352

AN:

1459664

Hom.:

1660

Cov.:

AF XY:

0.0458

AC XY:

33218

AN XY:

726036

show subpopulations

African (AFR)

AF:

0.00679

AC:

227

AN:

33444

American (AMR)

AF:

0.0249

AC:

1111

AN:

44610

Ashkenazi Jewish (ASJ)

AF:

0.0433

AC:

1129

AN:

26064

East Asian (EAS)

AF:

0.000126

AC:

AN:

39580

South Asian (SAS)

AF:

0.0460

AC:

3960

AN:

86084

European-Finnish (FIN)

AF:

0.0750

AC:

4001

AN:

53356

Middle Eastern (MID)

AF:

0.0687

AC:

395

AN:

5748

European-Non Finnish (NFE)

AF:

0.0475

AC:

52730

AN:

1110518

Other (OTH)

AF:

0.0464

AC:

2794

AN:

60260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

2916

5832

8748

11664

14580

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1890

3780

5670

7560

9450

<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:

0.0362

AC:

5511

AN:

152210

Hom.:

135

Cov.:

AF XY:

0.0370

AC XY:

2752

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.00847

AC:

352

AN:

41534

American (AMR)

AF:

0.0278

AC:

426

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.0455

AC:

158

AN:

3472

East Asian (EAS)

AF:

0.000772

AC:

AN:

5178

South Asian (SAS)

AF:

0.0468

AC:

226

AN:

4824

European-Finnish (FIN)

AF:

0.0757

AC:

802

AN:

10600

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0502

AC:

3415

AN:

67972

Other (OTH)

AF:

0.0379

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

287

573

860

1146

1433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0456

Hom.:

120

Bravo

AF:

0.0310

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jun 16, 2018

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. -

not specified

Benign:2

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

1268-13A>G in intron 6 of CEACAM16: This variant is not expected to have clinica l significance because it has been identified in 4.7% (391/8310) of European Ame rican chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs143934888). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.52

(source)

DANN

Benign

0.43

PhyloP100

-1.6

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