rs17802159

Variant names:

• chr4-111602-G-A
• rs17802159

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 0.759 in 151,966 control chromosomes in the GnomAD database, including 44,119 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 0.76 (44119 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.759 AC: 115275 AN: 151848 Hom.: 44061 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.759 AC: 115391 AN: 151966 Hom.: 44119 Cov.: 31 AF XY: 0.762 AC XY: 56597 AN XY: 74292

African (AFR) AF: 0.794 AC: 32892 AN: 41444

American (AMR) AF: 0.847 AC: 12936 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2873 AN: 3470

East Asian (EAS) AF: 0.963 AC: 4967 AN: 5158

South Asian (SAS) AF: 0.747 AC: 3594 AN: 4810

European-Finnish (FIN) AF: 0.683 AC: 7201 AN: 10542

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48290 AN: 67946

Other (OTH) AF: 0.795 AC: 1678 AN: 2112

Alfa AF: 0.745 Hom.: 52317

Bravo AF: 0.774

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17802159; hg19: chr4-111487;