rs894189

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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 id 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

GnomAD3 exomes

AF:

0.0913

AC:

22708

AN:

248662

Hom.:

1637

AF XY:

0.0855

AC XY:

11550

AN XY:

135034

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 SAS exome

AF:

0.0903

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

Gnomad4 AFR exome

AF:

0.251

Gnomad4 AMR exome

AF:

0.191

Gnomad4 ASJ exome

AF:

0.0597

Gnomad4 EAS exome

AF:

0.0484

Gnomad4 SAS exome

AF:

0.0897

Gnomad4 FIN exome

AF:

0.0605

Gnomad4 NFE exome

AF:

0.0530

Gnomad4 OTH exome

AF:

0.0763

GnomAD4 genome

AF:

0.118

AC:

17944

AN:

152210

Hom.:

1622

Cov.:

AF XY:

0.118

AC XY:

8794

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.243

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.0628

Gnomad4 EAS

AF:

0.0498

Gnomad4 SAS

AF:

0.0964

Gnomad4 FIN

AF:

0.0547

Gnomad4 NFE

AF:

0.0516

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0753

Hom.:

871

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. -

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). -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.016

DANN

Benign

0.67

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over