2-57462898-A-G

Variant names:

• chr2-57462898-A-G
• rs7589636

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 0.287 in 152,080 control chromosomes in the GnomAD database, including 6,733 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 0.29 (6733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.287 AC: 43592 AN: 151962 Hom.: 6726 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.287 AC: 43628 AN: 152080 Hom.: 6733 Cov.: 32 AF XY: 0.295 AC XY: 21928 AN XY: 74338

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.276

Alfa AF: 0.231 Hom.: 8584

Bravo AF: 0.295

Asia WGS AF: 0.305 AC: 1056 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7589636; hg19: chr2-57690033;