rs7591386

chr2-35621548-T-C

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 0.928 in 152,046 control chromosomes in the GnomAD database, including 65,834 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 0.93 (65834 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.97 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: 0.928 AC: 141043 AN: 151928 Hom.: 65793 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.928 AC: 141143 AN: 152046 Hom.: 65834 Cov.: 31 AF XY: 0.928 AC XY: 68973 AN XY: 74316

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.926

Alfa AF: 0.965 Hom.: 38002

Bravo AF: 0.923

Asia WGS AF: 0.865 AC: 3009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.17
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7591386; hg19: chr2-35846614;