rs2746112

Variant names:

• chrX-137531061-C-T
• rs2746112

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;