rs2213712

Variant names:

• chr1-172630738-G-C
• rs2213712

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 0.745 in 152,134 control chromosomes in the GnomAD database, including 43,162 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 0.75 (43162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 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: 0.745 AC: 113229 AN: 152016 Hom.: 43099 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.745 AC: 113349 AN: 152134 Hom.: 43162 Cov.: 32 AF XY: 0.745 AC XY: 55430 AN XY: 74356

African (AFR) AF: 0.907 AC: 37691 AN: 41538

American (AMR) AF: 0.674 AC: 10297 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2520 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3235 AN: 5170

South Asian (SAS) AF: 0.812 AC: 3920 AN: 4826

European-Finnish (FIN) AF: 0.691 AC: 7299 AN: 10568

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46028 AN: 67968

Other (OTH) AF: 0.737 AC: 1555 AN: 2110

Alfa AF: 0.713 Hom.: 4884

Bravo AF: 0.747

Asia WGS AF: 0.745 AC: 2593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2213712; hg19: chr1-172599878;