10-101219450-T-C

Variant names:

• chr10-101219450-T-C
• rs11190870

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.408 in 151,590 control chromosomes in the GnomAD database, including 12,796 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 0.41 (12796 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.60
• Publications: 65 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.408 AC: 61802 AN: 151470 Hom.: 12787 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.408 AC: 61839 AN: 151590 Hom.: 12796 Cov.: 30 AF XY: 0.401 AC XY: 29713 AN XY: 74056

African (AFR) AF: 0.420 AC: 17329 AN: 41264

American (AMR) AF: 0.350 AC: 5332 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3466

East Asian (EAS) AF: 0.460 AC: 2360 AN: 5126

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4808

European-Finnish (FIN) AF: 0.339 AC: 3546 AN: 10468

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29138 AN: 67906

Other (OTH) AF: 0.389 AC: 819 AN: 2106

Alfa AF: 0.421 Hom.: 60354

Bravo AF: 0.414

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	23
DANN	Benign	0.88
PhyloP100		7.6

Splicing

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

Other links and lift over

dbSNP: rs11190870; hg19: chr10-102979207;