chr10-99522443-G-A

Variant names:

• chr10-99522443-G-A
• rs11190134

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 0.361 in 152,086 control chromosomes in the GnomAD database, including 10,609 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 0.36 (10609 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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: 0.361 AC: 54894 AN: 151966 Hom.: 10595 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.361 AC: 54946 AN: 152086 Hom.: 10609 Cov.: 33 AF XY: 0.369 AC XY: 27444 AN XY: 74340

African (AFR) AF: 0.243 AC: 10086 AN: 41496

American (AMR) AF: 0.443 AC: 6768 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2743 AN: 5168

South Asian (SAS) AF: 0.377 AC: 1815 AN: 4816

European-Finnish (FIN) AF: 0.457 AC: 4833 AN: 10570

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26567 AN: 67974

Other (OTH) AF: 0.348 AC: 734 AN: 2108

Alfa AF: 0.380 Hom.: 30849

Bravo AF: 0.356

Asia WGS AF: 0.432 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs11190134; hg19: chr10-101282200;