X-138200029-G-T

Variant names:

• chrX-138200029-G-T
• rs609951

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 0.315 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0822 AC: 1926 AN: 23435

American (AMR) AF: 0.233 AC: 1905 AN: 8185

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 777 AN: 2318

East Asian (EAS) AF: 0.302 AC: 979 AN: 3243

South Asian (SAS) AF: 0.495 AC: 810 AN: 1635

European-Finnish (FIN) AF: 0.577 AC: 2724 AN: 4725

Middle Eastern (MID) AF: 0.367 AC: 69 AN: 188

European-Non Finnish (NFE) AF: 0.414 AC: 18960 AN: 45805

Other (OTH) AF: 0.326 AC: 411 AN: 1259

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs609951; hg19: chrX-137282188;