rs375643696

chr9-41960804-CA-C

Variant summary

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

The NM_001201380.3(CNTNAP3B):c.1844del(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. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTNAP3B	NM_001201380.3	c.1844del	p.Leu615ArgfsTer10	frameshift_variant	12/24	ENST00000377561.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTNAP3B	ENST00000377561.7	c.1844del	p.Leu615ArgfsTer10	frameshift_variant	12/24	1	NM_001201380.3	P1

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

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

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;