rs7594220

Variant names:

• chr2-643320-G-A
• rs7594220

Your query was ambiguous. Multiple possible variants found:

• chr2-643320-G-A
• chr2-643320-G-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 0.821 in 151,910 control chromosomes in the GnomAD database, including 51,401 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 0.82 (51401 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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 (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: 0.822 AC: 124707 AN: 151792 Hom.: 51376 Cov.: 34

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.821 AC: 124789 AN: 151910 Hom.: 51401 Cov.: 34 AF XY: 0.825 AC XY: 61260 AN XY: 74244

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.826

Alfa AF: 0.833 Hom.: 8918

Bravo AF: 0.819

Asia WGS AF: 0.884 AC: 3075 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	0.90
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7594220; hg19: chr2-643320;