rs17186196

Variant names:

• chr10-111072029-A-G
• rs17186196

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0868 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

Gnomad4 AFR AF: 0.0676

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.0939

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0839 Hom.: 109

Bravo AF: 0.0848

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17186196; hg19: chr10-112831787;