rs2746112

Positions:

• chrX-137531061-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 0.451 in 111,049 control chromosomes in the GnomAD database, including 8,202 homozygotes. There are 15,150 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 0.45 (8202 hom., 15150 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.451 AC: 50085 AN: 110996 Hom.: 8200 Cov.: 23 AF XY: 0.455 AC XY: 15139 AN XY: 33264

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.451 AC: 50092 AN: 111049 Hom.: 8202 Cov.: 23 AF XY: 0.455 AC XY: 15150 AN XY: 33327

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.458

Alfa AF: 0.459 Hom.: 4264

Bravo AF: 0.449

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2746112; hg19: chrX-136613220;