rs7598285

Variant names:

• chr2-6365431-G-A
• rs7598285

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 0.571 in 151,986 control chromosomes in the GnomAD database, including 25,835 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 0.57 (25835 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.571 AC: 86764 AN: 151868 Hom.: 25805 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.571 AC: 86851 AN: 151986 Hom.: 25835 Cov.: 32 AF XY: 0.575 AC XY: 42719 AN XY: 74302

African (AFR) AF: 0.728 AC: 30175 AN: 41468

American (AMR) AF: 0.579 AC: 8837 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1793 AN: 3464

East Asian (EAS) AF: 0.672 AC: 3467 AN: 5160

South Asian (SAS) AF: 0.504 AC: 2432 AN: 4828

European-Finnish (FIN) AF: 0.533 AC: 5631 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32876 AN: 67932

Other (OTH) AF: 0.552 AC: 1163 AN: 2106

Alfa AF: 0.503 Hom.: 14292

Bravo AF: 0.581

Asia WGS AF: 0.562 AC: 1950 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	1.7
DANN	Benign	0.22
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs7598285; hg19: chr2-6505563;