2-631528-A-G

Variant names:

• chr2-631528-A-G
• rs7585056

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 0.852 in 151,934 control chromosomes in the GnomAD database, including 55,297 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 0.85 (55297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.852 AC: 129390 AN: 151808 Hom.: 55250 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.837

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.852 AC: 129498 AN: 151934 Hom.: 55297 Cov.: 32 AF XY: 0.855 AC XY: 63482 AN XY: 74260

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.845

Alfa AF: 0.848 Hom.: 9636

Bravo AF: 0.854

Asia WGS AF: 0.893 AC: 3071 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7585056; hg19: chr2-631528;