X-123858972-C-T

Variant names:

• chrX-123858972-C-T
• rs5958318

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.60 (13884 hom., 19224 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• Publications: 3 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.595 AC: 65423 AN: 109867 Hom.: 13884 Cov.: 22

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.594

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.593

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.595 AC: 65457 AN: 109921 Hom.: 13884 Cov.: 22 AF XY: 0.597 AC XY: 19224 AN XY: 32199

African (AFR) AF: 0.667 AC: 20135 AN: 30197

American (AMR) AF: 0.589 AC: 6067 AN: 10304

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1404 AN: 2626

East Asian (EAS) AF: 0.424 AC: 1475 AN: 3475

South Asian (SAS) AF: 0.569 AC: 1472 AN: 2589

European-Finnish (FIN) AF: 0.664 AC: 3797 AN: 5717

Middle Eastern (MID) AF: 0.604 AC: 128 AN: 212

European-Non Finnish (NFE) AF: 0.566 AC: 29799 AN: 52638

Other (OTH) AF: 0.594 AC: 893 AN: 1503

Alfa AF: 0.572 Hom.: 43700

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs5958318; hg19: chrX-122992822;