2-212539345-T-A

Variant names:

• chr2-212539345-T-A
• rs62626347

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.00183 AC: 45 AN: 24546

American (AMR) AF: 0.00287 AC: 33 AN: 11498

Ashkenazi Jewish (ASJ) AF: 0.000354 AC: 1 AN: 2822

East Asian (EAS) AF: 0.00 AC: 0 AN: 4892

South Asian (SAS) AF: 0.00163 AC: 6 AN: 3674

European-Finnish (FIN) AF: 0.0157 AC: 95 AN: 6048

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 232

European-Non Finnish (NFE) AF: 0.00799 AC: 428 AN: 53538

Other (OTH) AF: 0.00559 AC: 9 AN: 1610

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	19
DANN	Benign	0.90
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs62626347; hg19: chr2-213404069;