7-50457722-A-G

Position:

• chr7-50457722-A-G

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 0.664 in 152,132 control chromosomes in the GnomAD database, including 33,982 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 0.66 (33982 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100977 AN: 152014 Hom.: 33955 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.664 AC: 101053 AN: 152132 Hom.: 33982 Cov.: 34 AF XY: 0.661 AC XY: 49185 AN XY: 74366

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.688

Alfa AF: 0.680 Hom.: 3054

Bravo AF: 0.668

Asia WGS AF: 0.594 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.4
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4947510; hg19: chr7-50525420; COSMIC: COSV63568086; COSMIC: COSV63568086;