10-111072029-A-G

Variant names:

• chr10-111072029-A-G
• rs17186196

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 0.0869 in 152,332 control chromosomes in the GnomAD database, including 627 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 0.087 (627 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0949 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: 0.0868 AC: 13214 AN: 152214 Hom.: 620 Cov.: 33

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0538

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0968

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0869 AC: 13237 AN: 152332 Hom.: 627 Cov.: 33 AF XY: 0.0875 AC XY: 6519 AN XY: 74488

African (AFR) AF: 0.0676 AC: 2811 AN: 41586

American (AMR) AF: 0.0738 AC: 1130 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.0535 AC: 278 AN: 5192

South Asian (SAS) AF: 0.0939 AC: 453 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1100 AN: 10610

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6588 AN: 68018

Other (OTH) AF: 0.114 AC: 242 AN: 2116

Alfa AF: 0.0829 Hom.: 110

Bravo AF: 0.0848

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.3
DANN	Benign	0.83
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs17186196; hg19: chr10-112831787;