19-44701052-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001039213.4(CEACAM16):c.-96-309C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,114 control chromosomes in the GnomAD database, including 22,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.50 (22408 hom., cov: 32)
• Consequence: CEACAM16 NM_001039213.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.558

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

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 19-44701052-C-A is Benign according to our data. Variant chr19-44701052-C-A is described in ClinVar as [Benign]. Clinvar id is 1225632.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM16	NM_001039213.4	c.-96-309C>A		intron_variant		ENST00000587331.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM16	ENST00000587331.7	c.-96-309C>A		intron_variant		1	NM_001039213.4	P1
CEACAM16-AS1	ENST00000662585.1	n.382-1875G>T		intron_variant, non_coding_transcript_variant
CEACAM16-AS1	ENST00000590796.1	n.315-1875G>T		intron_variant, non_coding_transcript_variant		5
CEACAM16-AS1	ENST00000702856.1	n.348-1875G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76573 AN: 151996 Hom.: 22362 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.519

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.504 AC: 76656 AN: 152114 Hom.: 22408 Cov.: 32 AF XY: 0.502 AC XY: 37330 AN XY: 74342

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.515

Alfa AF: 0.426 Hom.: 2364

Bravo AF: 0.539

Asia WGS AF: 0.456 AC: 1583 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.12
Dann	Benign	0.50

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

Other links and lift over

dbSNP: rs2919847; hg19: chr19-45204322;