X-140619338-T-G

Position:

• chrX-140619338-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;