rs62626347

Positions:

• chr2-212539345-T-A
• chr2-212539345-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The variant allele was found at a frequency of 0.00563 in 109,618 control chromosomes in the GnomAD database, including 8 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 0.0056 (8 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00563 AC: 617 AN: 109602 Hom.: 8 Cov.: 25

Gnomad AFR AF: 0.00184

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00287

Gnomad ASJ AF: 0.000354

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00163

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00799

Gnomad OTH AF: 0.00566

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

GnomAD4 genome AF: 0.00563 AC: 617 AN: 109618 Hom.: 8 Cov.: 25 AF XY: 0.00543 AC XY: 287 AN XY: 52824

Gnomad4 AFR AF: 0.00183

Gnomad4 AMR AF: 0.00287

Gnomad4 ASJ AF: 0.000354

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00163

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.00799

Gnomad4 OTH AF: 0.00559

Alfa AF: 0.00149 Hom.: 2

Bravo AF: 0.00418

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	19
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62626347; hg19: chr2-213404069;