rs17131683

Variant names:

• chr1-93015801-A-G
• rs17131683

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 0.0841 in 152,276 control chromosomes in the GnomAD database, including 591 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 0.084 (591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0954 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: 0.0841 AC: 12797 AN: 152158 Hom.: 590 Cov.: 32

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0664

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.00538

Gnomad SAS AF: 0.0591

Gnomad FIN AF: 0.0797

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0751

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

GnomAD4 genome AF: 0.0841 AC: 12801 AN: 152276 Hom.: 591 Cov.: 32 AF XY: 0.0810 AC XY: 6032 AN XY: 74458

African (AFR) AF: 0.0876 AC: 3641 AN: 41548

American (AMR) AF: 0.0663 AC: 1014 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3472

East Asian (EAS) AF: 0.00539 AC: 28 AN: 5192

South Asian (SAS) AF: 0.0594 AC: 286 AN: 4818

European-Finnish (FIN) AF: 0.0797 AC: 845 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6623 AN: 68028

Other (OTH) AF: 0.0743 AC: 157 AN: 2112

Alfa AF: 0.0934 Hom.: 232

Bravo AF: 0.0840

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
DANN	Benign	0.76
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs17131683; hg19: chr1-93481358;