rs5935729

Variant names:

• chrX-14323118-C-T
• rs5935729

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 0.438 in 110,782 control chromosomes in the GnomAD database, including 7,824 homozygotes. There are 14,230 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 0.44 (7824 hom., 14230 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.438 AC: 48537 AN: 110727 Hom.: 7823 Cov.: 23

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.438 AC: 48552 AN: 110782 Hom.: 7824 Cov.: 23 AF XY: 0.430 AC XY: 14230 AN XY: 33060

African (AFR) AF: 0.531 AC: 16175 AN: 30481

American (AMR) AF: 0.324 AC: 3408 AN: 10521

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 998 AN: 2638

East Asian (EAS) AF: 0.221 AC: 770 AN: 3483

South Asian (SAS) AF: 0.480 AC: 1246 AN: 2595

European-Finnish (FIN) AF: 0.453 AC: 2647 AN: 5839

Middle Eastern (MID) AF: 0.365 AC: 77 AN: 211

European-Non Finnish (NFE) AF: 0.422 AC: 22302 AN: 52831

Other (OTH) AF: 0.400 AC: 606 AN: 1516

Alfa AF: 0.423 Hom.: 52474

Bravo AF: 0.428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0050
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs5935729; hg19: chrX-14341240;