rs7591386

Variant names:

• chr2-35621548-T-C
• rs7591386

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 0.928 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.830 AC: 34369 AN: 41432

American (AMR) AF: 0.954 AC: 14568 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3373 AN: 3470

East Asian (EAS) AF: 0.914 AC: 4714 AN: 5156

South Asian (SAS) AF: 0.897 AC: 4326 AN: 4822

European-Finnish (FIN) AF: 0.974 AC: 10312 AN: 10590

Middle Eastern (MID) AF: 0.938 AC: 274 AN: 292

European-Non Finnish (NFE) AF: 0.976 AC: 66381 AN: 67984

Other (OTH) AF: 0.926 AC: 1960 AN: 2116

Alfa AF: 0.962 Hom.: 46810

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
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs7591386; hg19: chr2-35846614;