rs62120572

chr19-44710480-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001039213.4(CEACAM16):c.1268-16C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,611,444 control chromosomes in the GnomAD database, including 1,854 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.042 (169 hom., cov: 33)
  • Exomes 𝑓: 0.046 (1685 hom.)
• Consequence: CEACAM16 NM_001039213.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.02

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 19-44710480-C-T is Benign according to our data. Variant chr19-44710480-C-T is described in ClinVar as [Benign]. Clinvar id is 257226.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM16	NM_001039213.4	c.1268-16C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000587331.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM16	ENST00000587331.7	c.1268-16C>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001039213.4	P1
CEACAM16-AS1	ENST00000662585.1	n.382-11303G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0418 AC: 6357 AN: 152130 Hom.: 169 Cov.: 33

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0666

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0449

GnomAD3 exomes AF: 0.0428 AC: 10575 AN: 247160 Hom.: 278 AF XY: 0.0458 AC XY: 6146 AN XY: 134118

Gnomad AFR exome AF: 0.0343

Gnomad AMR exome AF: 0.0190

Gnomad ASJ exome AF: 0.0321

Gnomad EAS exome AF: 0.000393

Gnomad SAS exome AF: 0.0694

Gnomad FIN exome AF: 0.0438

Gnomad NFE exome AF: 0.0514

Gnomad OTH exome AF: 0.0438

GnomAD4 exome AF: 0.0461 AC: 67297 AN: 1459196 Hom.: 1685 Cov.: 31 AF XY: 0.0474 AC XY: 34378 AN XY: 725754

Gnomad4 AFR exome AF: 0.0377

Gnomad4 AMR exome AF: 0.0209

Gnomad4 ASJ exome AF: 0.0321

Gnomad4 EAS exome AF: 0.000253

Gnomad4 SAS exome AF: 0.0701

Gnomad4 FIN exome AF: 0.0471

Gnomad4 NFE exome AF: 0.0477

Gnomad4 OTH exome AF: 0.0408

GnomAD4 genome AF: 0.0418 AC: 6359 AN: 152248 Hom.: 169 Cov.: 33 AF XY: 0.0420 AC XY: 3126 AN XY: 74432

Gnomad4 AFR AF: 0.0341

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0502

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0446 Hom.: 43

Bravo AF: 0.0385

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 22, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	10
Dann	Benign	0.56

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: rs62120572; hg19: chr19-45213752;