rs17662433

Positions:

• chr17-51533026-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 115 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.00735

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0173

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0335 Hom.: 19

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17662433; hg19: chr17-49610387;