rs12834774

Variant names:

• chrX-140619338-T-G
• rs12834774

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 0.102 in 110,875 control chromosomes in the GnomAD database, including 466 homozygotes. There are 3,092 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 0.10 (466 hom., 3092 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 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: 0.102 AC: 11294 AN: 110823 Hom.: 466 Cov.: 22 AF XY: 0.0933 AC XY: 3084 AN XY: 33037

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.00198

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.00422

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.102 AC: 11303 AN: 110875 Hom.: 466 Cov.: 22 AF XY: 0.0934 AC XY: 3092 AN XY: 33099

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0484

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.00198

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.107 Hom.: 5290

Bravo AF: 0.0967

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12834774; hg19: chrX-139701503;