rs1350063

Variant names:

• chr2-125937049-T-A
• rs1350063

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.198 in 151,704 control chromosomes in the GnomAD database, including 3,546 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 0.20 (3546 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 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: 0.198 AC: 29961 AN: 151572 Hom.: 3547 Cov.: 33

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.198 AC: 29971 AN: 151704 Hom.: 3546 Cov.: 33 AF XY: 0.199 AC XY: 14763 AN XY: 74144

African (AFR) AF: 0.0779 AC: 3236 AN: 41540

American (AMR) AF: 0.170 AC: 2587 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3460

East Asian (EAS) AF: 0.125 AC: 646 AN: 5148

South Asian (SAS) AF: 0.307 AC: 1471 AN: 4792

European-Finnish (FIN) AF: 0.276 AC: 2914 AN: 10546

Middle Eastern (MID) AF: 0.186 AC: 35 AN: 188

European-Non Finnish (NFE) AF: 0.263 AC: 17846 AN: 67766

Other (OTH) AF: 0.190 AC: 397 AN: 2090

Alfa AF: 0.226 Hom.: 559

Bravo AF: 0.182

Asia WGS AF: 0.169 AC: 577 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1350063; hg19: chr2-126694626;