rs4731279

chr7-125983088-C-T

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 0.769 in 151,882 control chromosomes in the GnomAD database, including 45,030 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 0.77 (45030 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116692 AN: 151764 Hom.: 45007 Cov.: 30

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.769 AC: 116754 AN: 151882 Hom.: 45030 Cov.: 30 AF XY: 0.768 AC XY: 57014 AN XY: 74234

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.782

Alfa AF: 0.790 Hom.: 95259

Bravo AF: 0.771

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731279; hg19: chr7-125623142;