rs5975178

Variant names:

• chrX-130270608-C-T
• rs5975178

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.541 in 110,691 control chromosomes in the GnomAD database, including 12,809 homozygotes. There are 17,659 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 0.54 (12809 hom., 17659 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.541 AC: 59860 AN: 110637 Hom.: 12809 Cov.: 23 AF XY: 0.536 AC XY: 17595 AN XY: 32855

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.541 AC: 59921 AN: 110691 Hom.: 12809 Cov.: 23 AF XY: 0.536 AC XY: 17659 AN XY: 32919

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.541

Alfa AF: 0.490 Hom.: 3583

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5975178; hg19: chrX-129404582;