2-70796300-T-C

Variant names:

• chr2-70796300-T-C
• rs1122616

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 0.691 in 151,208 control chromosomes in the GnomAD database, including 37,906 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 0.69 (37906 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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: 0.691 AC: 104417 AN: 151104 Hom.: 37859 Cov.: 27

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.691 AC: 104521 AN: 151208 Hom.: 37906 Cov.: 27 AF XY: 0.698 AC XY: 51537 AN XY: 73826

African (AFR) AF: 0.906 AC: 37378 AN: 41234

American (AMR) AF: 0.677 AC: 10309 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1933 AN: 3470

East Asian (EAS) AF: 0.907 AC: 4632 AN: 5106

South Asian (SAS) AF: 0.688 AC: 3289 AN: 4784

European-Finnish (FIN) AF: 0.674 AC: 6977 AN: 10356

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.559 AC: 37833 AN: 67738

Other (OTH) AF: 0.685 AC: 1434 AN: 2094

Alfa AF: 0.627 Hom.: 3919

Bravo AF: 0.705

Asia WGS AF: 0.792 AC: 2752 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1122616; hg19: chr2-71023432;