chr5-91925830-G-T

Variant names:

• chr5-91925830-G-T
• rs10063941

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 0.834 in 152,096 control chromosomes in the GnomAD database, including 53,046 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 0.83 (53046 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 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: 0.833 AC: 126659 AN: 151978 Hom.: 52989 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.834 AC: 126779 AN: 152096 Hom.: 53046 Cov.: 31 AF XY: 0.832 AC XY: 61855 AN XY: 74338

African (AFR) AF: 0.854 AC: 35426 AN: 41496

American (AMR) AF: 0.799 AC: 12199 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2971 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3115 AN: 5158

South Asian (SAS) AF: 0.816 AC: 3934 AN: 4824

European-Finnish (FIN) AF: 0.834 AC: 8811 AN: 10568

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57502 AN: 67990

Other (OTH) AF: 0.837 AC: 1767 AN: 2110

Alfa AF: 0.846 Hom.: 27580

Bravo AF: 0.830

Asia WGS AF: 0.775 AC: 2699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.3
DANN	Benign	0.59
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10063941; hg19: chr5-91221647;