rs17190526

Variant names:

• chr6-31114304-G-A
• rs17190526

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 0.0822 in 147,126 control chromosomes in the GnomAD database, including 519 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 0.082 (519 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.094 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: 0.0822 AC: 12077 AN: 147004 Hom.: 517 Cov.: 26

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0491

Gnomad EAS AF: 0.0695

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0548

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0822 AC: 12093 AN: 147126 Hom.: 519 Cov.: 26 AF XY: 0.0798 AC XY: 5700 AN XY: 71450

African (AFR) AF: 0.0795 AC: 3188 AN: 40078

American (AMR) AF: 0.0633 AC: 927 AN: 14640

Ashkenazi Jewish (ASJ) AF: 0.0491 AC: 167 AN: 3400

East Asian (EAS) AF: 0.0697 AC: 335 AN: 4806

South Asian (SAS) AF: 0.0648 AC: 295 AN: 4552

European-Finnish (FIN) AF: 0.0518 AC: 500 AN: 9652

Middle Eastern (MID) AF: 0.0556 AC: 16 AN: 288

European-Non Finnish (NFE) AF: 0.0959 AC: 6404 AN: 66766

Other (OTH) AF: 0.0727 AC: 149 AN: 2050

Alfa AF: 0.0876 Hom.: 988

Bravo AF: 0.0829

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.32
PhyloP100		0.39
PromoterAI		0.068	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17190526; hg19: chr6-31082081;