rs792106

Variant names:

• chr2-5391399-G-A
• rs792106

Your query was ambiguous. Multiple possible variants found:

• chr2-5391399-G-A
• chr2-5391399-G-C

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 0.384 in 152,074 control chromosomes in the GnomAD database, including 12,431 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 0.38 (12431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58340 AN: 151956 Hom.: 12437 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.384 AC: 58331 AN: 152074 Hom.: 12431 Cov.: 32 AF XY: 0.381 AC XY: 28301 AN XY: 74344

African (AFR) AF: 0.178 AC: 7395 AN: 41508

American (AMR) AF: 0.398 AC: 6073 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1687 AN: 3472

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5160

South Asian (SAS) AF: 0.356 AC: 1717 AN: 4818

European-Finnish (FIN) AF: 0.422 AC: 4458 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32982 AN: 67958

Other (OTH) AF: 0.397 AC: 838 AN: 2112

Alfa AF: 0.449 Hom.: 21402

Bravo AF: 0.379

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs792106; hg19: chr2-5531532;