7-113347595-C-T

Variant names:

• chr7-113347595-C-T
• rs4476935

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.402 in 151,706 control chromosomes in the GnomAD database, including 12,658 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (12658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60971 AN: 151588 Hom.: 12657 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.402 AC: 60984 AN: 151706 Hom.: 12658 Cov.: 32 AF XY: 0.399 AC XY: 29575 AN XY: 74106

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.389

Alfa AF: 0.431 Hom.: 19208

Bravo AF: 0.401

Asia WGS AF: 0.393 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.031
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4476935; hg19: chr7-112987650; COSMIC: COSV68673476;