rs812810

Variant names:

• chr2-7746748-C-T
• rs812810

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 0.902 in 152,186 control chromosomes in the GnomAD database, including 61,930 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 0.90 (61930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.902 AC: 137143 AN: 152068 Hom.: 61893 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.902 AC: 137231 AN: 152186 Hom.: 61930 Cov.: 31 AF XY: 0.901 AC XY: 67055 AN XY: 74408

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.900

Alfa AF: 0.913 Hom.: 83322

Bravo AF: 0.900

Asia WGS AF: 0.911 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs812810; hg19: chr2-7886879;