10-95071450-C-T

Variant names:

• chr10-95071450-C-T
• rs11188172

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 0.182 in 152,112 control chromosomes in the GnomAD database, including 3,227 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 0.18 (3227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27669 AN: 151994 Hom.: 3222 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.182 AC: 27672 AN: 152112 Hom.: 3227 Cov.: 32 AF XY: 0.185 AC XY: 13757 AN XY: 74380

African (AFR) AF: 0.0436 AC: 1811 AN: 41540

American (AMR) AF: 0.254 AC: 3876 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3464

East Asian (EAS) AF: 0.0845 AC: 437 AN: 5174

South Asian (SAS) AF: 0.191 AC: 921 AN: 4816

European-Finnish (FIN) AF: 0.294 AC: 3104 AN: 10566

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

European-Non Finnish (NFE) AF: 0.239 AC: 16265 AN: 67968

Other (OTH) AF: 0.163 AC: 343 AN: 2108

Alfa AF: 0.204 Hom.: 843

Bravo AF: 0.170

Asia WGS AF: 0.118 AC: 411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.054
DANN	Benign	0.50
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs11188172; hg19: chr10-96831207;