chr19-44703201-T-TCC

Variant names:

• chr19-44703201-T-TCC
• rs201962453
• NM_001039213.4:c.38-148_38-147insCC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001039213.4(CEACAM16):​c.38-148_38-147insCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00248 in 631,392 control chromosomes in the GnomAD database, including 26 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0072 (17 hom., cov: 33)
  • Exomes 𝑓: 0.0010 (9 hom.)
• Consequence: CEACAM16 NM_001039213.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.582
• Publications: 0 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 -10 ACMG points.

• BP6: Variant 19-44703201-T-TCC is Benign according to our data. Variant chr19-44703201-T-TCC is described in ClinVar as Likely_benign. ClinVar VariationId is 1197717.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00715 (1089/152302) while in subpopulation AFR AF = 0.0241 (1001/41554). AF 95% confidence interval is 0.0229. There are 17 homozygotes in GnomAd4. There are 514 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 17 AR,AD gene

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.38-148_38-147insCC		intron	N/A	NP_001034302.2	Q2WEN9
	CEACAM16-AS1	NR_186815.1		n.348-4025_348-4024insGG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16	ENST00000587331.7	TSL:1 MANE Select	c.38-148_38-147insCC		intron	N/A	ENSP00000466561.1	Q2WEN9
	CEACAM16	ENST00000405314.2	TSL:5	c.38-148_38-147insCC		intron	N/A	ENSP00000385576.1	Q2WEN9
	CEACAM16-AS1	ENST00000590796.1	TSL:5	n.315-4025_315-4024insGG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00715 AC: 1088 AN: 152184 Hom.: 17 Cov.: 33

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00445

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.00622

GnomAD4 exome AF: 0.00100 AC: 480 AN: 479090 Hom.: 9 AF XY: 0.000843 AC XY: 208 AN XY: 246614

African (AFR) AF: 0.0248 AC: 327 AN: 13166

American (AMR) AF: 0.00341 AC: 62 AN: 18166

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13216

East Asian (EAS) AF: 0.00 AC: 0 AN: 30960

South Asian (SAS) AF: 0.0000537 AC: 2 AN: 37224

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34906

Middle Eastern (MID) AF: 0.00101 AC: 2 AN: 1986

European-Non Finnish (NFE) AF: 0.0000561 AC: 17 AN: 303000

Other (OTH) AF: 0.00264 AC: 70 AN: 26466

GnomAD4 genome AF: 0.00715 AC: 1089 AN: 152302 Hom.: 17 Cov.: 33 AF XY: 0.00690 AC XY: 514 AN XY: 74472

African (AFR) AF: 0.0241 AC: 1001 AN: 41554

American (AMR) AF: 0.00445 AC: 68 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000882 AC: 6 AN: 68024

Other (OTH) AF: 0.00616 AC: 13 AN: 2112

Alfa AF: 0.00527 Hom.: 1

Bravo AF: 0.00878

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs201962453; hg19: chr19-45206471;