rs2213712

chr1-172630738-G-C

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 0.745 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2213712; hg19: chr1-172599878;