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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.614

Alfa AF: 0.695 Hom.: 73019

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2970836; hg19: chr12-19259778;