rs17761467

Variant names:

• chr17-1902383-G-A
• rs17761467

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 0.118 in 152,270 control chromosomes in the GnomAD database, including 1,322 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 0.12 (1322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.118 AC: 18014 AN: 152152 Hom.: 1323 Cov.: 32

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.118 AC: 18015 AN: 152270 Hom.: 1322 Cov.: 32 AF XY: 0.116 AC XY: 8673 AN XY: 74456

African (AFR) AF: 0.0381 AC: 1585 AN: 41554

American (AMR) AF: 0.108 AC: 1656 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3472

East Asian (EAS) AF: 0.0697 AC: 361 AN: 5180

South Asian (SAS) AF: 0.0800 AC: 386 AN: 4828

European-Finnish (FIN) AF: 0.121 AC: 1282 AN: 10608

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11501 AN: 68008

Other (OTH) AF: 0.140 AC: 297 AN: 2116

Alfa AF: 0.117 Hom.: 468

Bravo AF: 0.114

Asia WGS AF: 0.0960 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs17761467; hg19: chr17-1805677;