X-140153333-C-T

Variant names:

• chrX-140153333-C-T
• rs677033

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 0.391 in 110,784 control chromosomes in the GnomAD database, including 7,223 homozygotes. There are 12,990 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 0.39 (7223 hom., 12990 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 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: 0.391 AC: 43323 AN: 110733 Hom.: 7220 Cov.: 23 AF XY: 0.394 AC XY: 12989 AN XY: 32969

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.391 AC: 43321 AN: 110784 Hom.: 7223 Cov.: 23 AF XY: 0.393 AC XY: 12990 AN XY: 33030

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.406

Alfa AF: 0.472 Hom.: 11789

Bravo AF: 0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs677033; hg19: chrX-139235492;