10-95568939-C-T

Variant names:

• chr10-95568939-C-T
• rs500470

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 0.478 in 152,134 control chromosomes in the GnomAD database, including 20,618 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 0.48 (20618 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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: 0.479 AC: 72762 AN: 152018 Hom.: 20621 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.478 AC: 72762 AN: 152134 Hom.: 20618 Cov.: 33 AF XY: 0.479 AC XY: 35596 AN XY: 74374

African (AFR) AF: 0.157 AC: 6522 AN: 41506

American (AMR) AF: 0.582 AC: 8894 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2735 AN: 5168

South Asian (SAS) AF: 0.407 AC: 1963 AN: 4826

European-Finnish (FIN) AF: 0.647 AC: 6853 AN: 10586

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42522 AN: 67974

Other (OTH) AF: 0.469 AC: 992 AN: 2116

Alfa AF: 0.526 Hom.: 3068

Bravo AF: 0.464

Asia WGS AF: 0.441 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.0
DANN	Benign	0.74
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs500470; hg19: chr10-97328696;