10-8475697-C-T

Variant names:

• chr10-8475697-C-T
• rs7085991

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 0.309 in 151,970 control chromosomes in the GnomAD database, including 7,849 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 0.31 (7849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.309 AC: 46895 AN: 151852 Hom.: 7838 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.309 AC: 46929 AN: 151970 Hom.: 7849 Cov.: 31 AF XY: 0.317 AC XY: 23519 AN XY: 74268

African (AFR) AF: 0.293 AC: 12154 AN: 41428

American (AMR) AF: 0.430 AC: 6567 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3169 AN: 5142

South Asian (SAS) AF: 0.411 AC: 1982 AN: 4818

European-Finnish (FIN) AF: 0.260 AC: 2750 AN: 10566

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18102 AN: 67962

Other (OTH) AF: 0.321 AC: 677 AN: 2108

Alfa AF: 0.293 Hom.: 15109

Bravo AF: 0.320

Asia WGS AF: 0.529 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.48
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7085991; hg19: chr10-8517660;