rs17662433

Variant names:

• chr17-51533026-G-A
• rs17662433

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0285 in 152,114 control chromosomes in the GnomAD database, including 115 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 0.028 (115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0285 (4335/152114) while in subpopulation NFE AF = 0.0441 (2997/67998). AF 95% confidence interval is 0.0428. There are 115 homozygotes in GnomAd4. There are 1998 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 115 gene

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: 0.0285 AC: 4339 AN: 151996 Hom.: 115 Cov.: 32

Gnomad AFR AF: 0.00737

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0173

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0285 AC: 4335 AN: 152114 Hom.: 115 Cov.: 32 AF XY: 0.0269 AC XY: 1998 AN XY: 74346

African (AFR) AF: 0.00735 AC: 305 AN: 41484

American (AMR) AF: 0.0291 AC: 444 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4818

European-Finnish (FIN) AF: 0.0173 AC: 183 AN: 10572

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0441 AC: 2997 AN: 67998

Other (OTH) AF: 0.0421 AC: 89 AN: 2112

Alfa AF: 0.0338 Hom.: 56

Bravo AF: 0.0288

Asia WGS AF: 0.00635 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.8
DANN	Benign	0.80
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs17662433; hg19: chr17-49610387;