rs5975493

Positions:

• chrX-135042148-C-G
• chrX-135042148-C-T

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 0.415 in 109,066 control chromosomes in the GnomAD database, including 7,163 homozygotes. There are 12,393 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 0.42 (7163 hom., 12393 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

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: 0.416 AC: 45302 AN: 109018 Hom.: 7166 Cov.: 21 AF XY: 0.395 AC XY: 12374 AN XY: 31356

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.415 AC: 45313 AN: 109066 Hom.: 7163 Cov.: 21 AF XY: 0.395 AC XY: 12393 AN XY: 31414

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.417

Alfa AF: 0.244 Hom.: 1092

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5975493; hg19: chrX-134176178;