chrX-138200029-G-T

Position:

• chrX-138200029-G-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 0.315 in 91,383 control chromosomes in the GnomAD database, including 3,328 homozygotes. There are 8,674 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 0.32 (3328 hom., 8674 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.467 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: 0.315 AC: 28818 AN: 91362 Hom.: 3331 Cov.: 23 AF XY: 0.432 AC XY: 8668 AN XY: 20074

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.315 AC: 28811 AN: 91383 Hom.: 3328 Cov.: 23 AF XY: 0.432 AC XY: 8674 AN XY: 20101

Gnomad4 AFR AF: 0.0822

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.326

Alfa AF: 0.184 Hom.: 956

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs609951; hg19: chrX-137282188;