rs2970836

Variant names:

• chr12-19106844-A-G
• rs2970836

Your query was ambiguous. Multiple possible variants found:

• chr12-19106844-A-G
• chr12-19106844-A-T

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 0.584 in 152,122 control chromosomes in the GnomAD database, including 28,220 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 0.58 (28220 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.721 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: 0.585 AC: 88865 AN: 152004 Hom.: 28233 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.584 AC: 88838 AN: 152122 Hom.: 28220 Cov.: 33 AF XY: 0.580 AC XY: 43166 AN XY: 74390

African (AFR) AF: 0.341 AC: 14169 AN: 41498

American (AMR) AF: 0.562 AC: 8585 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3470

East Asian (EAS) AF: 0.387 AC: 2001 AN: 5176

South Asian (SAS) AF: 0.496 AC: 2392 AN: 4820

European-Finnish (FIN) AF: 0.741 AC: 7832 AN: 10572

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49360 AN: 67988

Other (OTH) AF: 0.614 AC: 1299 AN: 2114

Alfa AF: 0.672 Hom.: 110584

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.65
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2970836; hg19: chr12-19259778;