rs17302090

Variant names:

• chrX-67535561-G-A
• rs17302090

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 0.0831 in 111,032 control chromosomes in the GnomAD database, including 315 homozygotes. There are 2,476 hemizygotes in GnomAD. 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 0.083 (315 hom., 2476 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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: 0.0831 AC: 9219 AN: 110978 Hom.: 315 Cov.: 23

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0189

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0621

Gnomad EAS AF: 0.000567

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0831 AC: 9222 AN: 111032 Hom.: 315 Cov.: 23 AF XY: 0.0744 AC XY: 2476 AN XY: 33276

African (AFR) AF: 0.115 AC: 3500 AN: 30487

American (AMR) AF: 0.0633 AC: 661 AN: 10435

Ashkenazi Jewish (ASJ) AF: 0.0621 AC: 164 AN: 2640

East Asian (EAS) AF: 0.000569 AC: 2 AN: 3514

South Asian (SAS) AF: 0.0231 AC: 60 AN: 2603

European-Finnish (FIN) AF: 0.0525 AC: 312 AN: 5938

Middle Eastern (MID) AF: 0.0981 AC: 21 AN: 214

European-Non Finnish (NFE) AF: 0.0818 AC: 4335 AN: 52999

Other (OTH) AF: 0.102 AC: 154 AN: 1514

Alfa AF: 0.0836 Hom.: 6170

Bravo AF: 0.0854

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.55
DANN	Benign	0.76
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs17302090; hg19: chrX-66755403;