rs17186196

chr10-111072029-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;