chr7-113347595-C-T

Variant names:

• chr7-113347595-C-T
• rs4476935

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.317 AC: 13127 AN: 41380

American (AMR) AF: 0.401 AC: 6107 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1548 AN: 3458

East Asian (EAS) AF: 0.611 AC: 3133 AN: 5126

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4820

European-Finnish (FIN) AF: 0.378 AC: 3964 AN: 10500

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30285 AN: 67890

Other (OTH) AF: 0.389 AC: 818 AN: 2102

Alfa AF: 0.428 Hom.: 23755

Bravo AF: 0.401

Asia WGS AF: 0.393 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.031
DANN	Benign	0.46
PhyloP100		-2.0

Splicing

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

Other links and lift over

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