NM_001039213.4:c.941-14C>T

Variant names:

• chr19-44707847-C-T
• rs10426475
• NM_001039213.4:c.941-14C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001039213.4(CEACAM16):​c.941-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0418 in 1,514,672 control chromosomes in the GnomAD database, including 2,023 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.060 (393 hom., cov: 32)
  • Exomes 𝑓: 0.040 (1630 hom.)
• Consequence: CEACAM16 NM_001039213.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -0.207
• Publications: 1 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 19-44707847-C-T is Benign according to our data. Variant chr19-44707847-C-T is described in ClinVar as Benign. ClinVar VariationId is 226510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.124 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16	NM_001039213.4	MANE Select	c.941-14C>T		intron	N/A	NP_001034302.2
	CEACAM16-AS1	NR_186815.1		n.348-8670G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16	ENST00000587331.7	TSL:1 MANE Select	c.941-14C>T		intron	N/A	ENSP00000466561.1
	CEACAM16	ENST00000405314.2	TSL:5	c.941-14C>T		intron	N/A	ENSP00000385576.1
	CEACAM16-AS1	ENST00000590796.1	TSL:5	n.314+8103G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0595 AC: 9057 AN: 152106 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0311

Gnomad OTH AF: 0.0630

GnomAD2 exomes AF: 0.0636 AC: 10971 AN: 172482 AF XY: 0.0598

Gnomad AFR exome AF: 0.0891

Gnomad AMR exome AF: 0.177

Gnomad ASJ exome AF: 0.0263

Gnomad EAS exome AF: 0.0419

Gnomad FIN exome AF: 0.0516

Gnomad NFE exome AF: 0.0312

Gnomad OTH exome AF: 0.0510

GnomAD4 exome AF: 0.0399 AC: 54319 AN: 1362448 Hom.: 1630 Cov.: 29 AF XY: 0.0402 AC XY: 26763 AN XY: 665002

African (AFR) AF: 0.0877 AC: 2742 AN: 31264

American (AMR) AF: 0.170 AC: 5993 AN: 35250

Ashkenazi Jewish (ASJ) AF: 0.0272 AC: 572 AN: 21038

East Asian (EAS) AF: 0.0486 AC: 1820 AN: 37446

South Asian (SAS) AF: 0.0745 AC: 5280 AN: 70896

European-Finnish (FIN) AF: 0.0496 AC: 2414 AN: 48692

Middle Eastern (MID) AF: 0.0374 AC: 175 AN: 4674

European-Non Finnish (NFE) AF: 0.0310 AC: 32807 AN: 1057142

Other (OTH) AF: 0.0449 AC: 2516 AN: 56046

GnomAD4 genome AF: 0.0595 AC: 9061 AN: 152224 Hom.: 393 Cov.: 32 AF XY: 0.0622 AC XY: 4626 AN XY: 74426

African (AFR) AF: 0.0863 AC: 3584 AN: 41530

American (AMR) AF: 0.128 AC: 1962 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0308 AC: 107 AN: 3470

East Asian (EAS) AF: 0.0510 AC: 264 AN: 5180

South Asian (SAS) AF: 0.0805 AC: 389 AN: 4832

European-Finnish (FIN) AF: 0.0451 AC: 478 AN: 10596

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0311 AC: 2115 AN: 68016

Other (OTH) AF: 0.0619 AC: 131 AN: 2116

Alfa AF: 0.0432 Hom.: 376

Bravo AF: 0.0680

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Jul 01, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not specified Benign:2

Nov 24, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

941-14C>T in intron 5 of CEACAM16: This variant is not expected to have clinical significance because it has been identified in 8.2% (354/4340) of African Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs10426475).

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.78
DANN	Benign	0.40
PhyloP100		-0.21
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

Other links and lift over

dbSNP: rs10426475; hg19: chr19-45211119;