X-138200029-G-T

Variant names:

• chrX-138200029-G-T
• rs609951

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;