rs812810

chr2-7746748-C-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 0.902 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;