rs5934508

Variant names:

• chrX-8950735-C-T
• rs5934508

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 0.482 in 111,066 control chromosomes in the GnomAD database, including 9,547 homozygotes. There are 15,707 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 0.48 (9547 hom., 15707 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 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: 0.482 AC: 53528 AN: 111014 Hom.: 9549 Cov.: 23

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.482 AC: 53550 AN: 111066 Hom.: 9547 Cov.: 23 AF XY: 0.472 AC XY: 15707 AN XY: 33310

African (AFR) AF: 0.612 AC: 18692 AN: 30564

American (AMR) AF: 0.355 AC: 3733 AN: 10529

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 1523 AN: 2636

East Asian (EAS) AF: 0.452 AC: 1583 AN: 3504

South Asian (SAS) AF: 0.584 AC: 1543 AN: 2640

European-Finnish (FIN) AF: 0.352 AC: 2065 AN: 5866

Middle Eastern (MID) AF: 0.526 AC: 110 AN: 209

European-Non Finnish (NFE) AF: 0.441 AC: 23362 AN: 52918

Other (OTH) AF: 0.499 AC: 763 AN: 1528

Alfa AF: 0.456 Hom.: 38318

Bravo AF: 0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.53
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs5934508; hg19: chrX-8918776;