rs375643696

Variant names:

• chr9-41960804-CA-C
• rs375643696
• NM_001201380.3:c.1844delT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS1

The NM_001201380.3(CNTNAP3B):​c.1844delT​(p.Leu615ArgfsTer10) variant causes a frameshift change. The variant allele was found at a frequency of 0.00348 in 151,468 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.0035 (0 hom., cov: 48)
  • Exomes 𝑓: 0.0047 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CNTNAP3B NM_001201380.3 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 6.32

Genes affected

CNTNAP3B (HGNC:32035): (contactin associated protein family member 3B) Predicted to be involved in cell adhesion. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 9-41960804-CA-C is Benign according to our data. Variant chr9-41960804-CA-C is described in ClinVar as [Benign]. Clinvar id is 402551.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00348 (527/151468) while in subpopulation SAS AF= 0.0425 (193/4536). AF 95% confidence interval is 0.0376. There are 0 homozygotes in gnomad4. There are 319 alleles in male gnomad4 subpopulation. Median coverage is 48. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTNAP3B	NM_001201380.3	c.1844delT	p.Leu615ArgfsTer10	frameshift_variant	Exon 12 of 24	ENST00000377561.7	NP_001188309.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP3B	ENST00000377561.7	c.1844delT	p.Leu615ArgfsTer10	frameshift_variant	Exon 12 of 24	1	NM_001201380.3	ENSP00000478671.2

Frequencies

GnomAD3 genomes AF: 0.00350 AC: 530 AN: 151348 Hom.: 0 Cov.: 48

Gnomad AFR AF: 0.000434

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00243

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.00568

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00210

Gnomad OTH AF: 0.00434

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00466 AC: 6718 AN: 1442056 Hom.: 0 Cov.: 35 AF XY: 0.00577 AC XY: 4133 AN XY: 715978

Gnomad4 AFR exome AF: 0.000577

Gnomad4 AMR exome AF: 0.00201

Gnomad4 ASJ exome AF: 0.0229

Gnomad4 EAS exome AF: 0.0131

Gnomad4 SAS exome AF: 0.0387

Gnomad4 FIN exome AF: 0.000226

Gnomad4 NFE exome AF: 0.00179

Gnomad4 OTH exome AF: 0.00615

GnomAD4 genome AF: 0.00348 AC: 527 AN: 151468 Hom.: 0 Cov.: 48 AF XY: 0.00431 AC XY: 319 AN XY: 73968

Gnomad4 AFR AF: 0.000433

Gnomad4 AMR AF: 0.00243

Gnomad4 ASJ AF: 0.0286

Gnomad4 EAS AF: 0.00569

Gnomad4 SAS AF: 0.0425

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00210

Gnomad4 OTH AF: 0.00429

Alfa AF: 0.00645 Hom.: 2

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs375643696; hg19: chr9-65595156;