rs17090919

Variant names:

• chr10-113731471-G-A
• rs17090919

Your query was ambiguous. Multiple possible variants found:

• chr10-113731471-G-A
• chr10-113731471-G-C

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 0.0866 in 152,138 control chromosomes in the GnomAD database, including 696 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 (696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13171 AN: 152020 Hom.: 696 Cov.: 32

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0697

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0866 AC: 13168 AN: 152138 Hom.: 696 Cov.: 32 AF XY: 0.0854 AC XY: 6354 AN XY: 74390

African (AFR) AF: 0.0516 AC: 2141 AN: 41512

American (AMR) AF: 0.0529 AC: 808 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3468

East Asian (EAS) AF: 0.126 AC: 650 AN: 5170

South Asian (SAS) AF: 0.127 AC: 613 AN: 4814

European-Finnish (FIN) AF: 0.0697 AC: 738 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7462 AN: 67986

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0956 Hom.: 1002

Bravo AF: 0.0840

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.96
DANN	Benign	0.43
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs17090919; hg19: chr10-115491230;