rs10094577

Variant names:

• chr8-42230058-T-C
• rs10094577

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 0.173 in 152,054 control chromosomes in the GnomAD database, including 4,800 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 0.17 (4800 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26217 AN: 151936 Hom.: 4773 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.173 AC: 26289 AN: 152054 Hom.: 4800 Cov.: 32 AF XY: 0.169 AC XY: 12544 AN XY: 74366

African (AFR) AF: 0.460 AC: 19061 AN: 41404

American (AMR) AF: 0.0906 AC: 1384 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0325 AC: 113 AN: 3472

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5188

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4812

European-Finnish (FIN) AF: 0.0291 AC: 309 AN: 10618

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3855 AN: 67976

Other (OTH) AF: 0.128 AC: 269 AN: 2106

Alfa AF: 0.0781 Hom.: 1728

Bravo AF: 0.184

Asia WGS AF: 0.198 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.1
DANN	Benign	0.68
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs10094577; hg19: chr8-42087576;