rs12834774

Variant names:

• chrX-140619338-T-G
• rs12834774

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.102 AC: 11294 AN: 110823 Hom.: 466 Cov.: 22

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

African (AFR) AF: 0.110 AC: 3365 AN: 30508

American (AMR) AF: 0.0484 AC: 504 AN: 10421

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 200 AN: 2650

East Asian (EAS) AF: 0.00198 AC: 7 AN: 3527

South Asian (SAS) AF: 0.0164 AC: 43 AN: 2620

European-Finnish (FIN) AF: 0.119 AC: 691 AN: 5815

Middle Eastern (MID) AF: 0.00463 AC: 1 AN: 216

European-Non Finnish (NFE) AF: 0.117 AC: 6195 AN: 52921

Other (OTH) AF: 0.0748 AC: 114 AN: 1525

Alfa AF: 0.107 Hom.: 6918

Bravo AF: 0.0967

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.26
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs12834774; hg19: chrX-139701503;