rs894189

Variant names:

• chr19-44703425-G-A
• rs894189
• NM_001039213.4:c.114G>A
• CEACAM16 p.Thr38Thr

Your query was ambiguous. Multiple possible variants found:

• chr19-44703425-G-A
• chr19-44703425-G-T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: -4.62
• Publications: 6 publications found

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039213.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16	NM_001039213.4	MANE Select	c.114G>A	p.Thr38Thr	synonymous	Exon 3 of 7	NP_001034302.2	Q2WEN9
	CEACAM16-AS1	NR_186815.1		n.348-4248C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16	ENST00000587331.7	TSL:1 MANE Select	c.114G>A	p.Thr38Thr	synonymous	Exon 3 of 7	ENSP00000466561.1	Q2WEN9
	CEACAM16	ENST00000405314.2	TSL:5	c.114G>A	p.Thr38Thr	synonymous	Exon 2 of 6	ENSP00000385576.1	Q2WEN9
	CEACAM16-AS1	ENST00000590796.1	TSL:5	n.315-4248C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17918 AN: 152092 Hom.: 1612 Cov.: 32

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

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.: 33 AF XY: 0.0647 AC XY: 47012 AN XY: 727032

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

GnomAD4 genome AF: 0.118 AC: 17944 AN: 152210 Hom.: 1622 Cov.: 32 AF XY: 0.118 AC XY: 8794 AN XY: 74438

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: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0516 AC: 3508 AN: 68018

Other (OTH) AF: 0.110 AC: 232 AN: 2114

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	4	not specified (4)
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.016
DANN	Benign	0.67
PhyloP100		-4.6
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs894189;

hg19: chr19-45206695;

COSMIC: COSV101312677;