chrX-15189904-C-T

Variant names:

• chrX-15189904-C-T
• rs1993969

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 0.55 (11895 hom., 17878 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.548 AC: 60406 AN: 110205 Hom.: 11897 Cov.: 23

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.565

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: 0.548 AC: 60436 AN: 110255 Hom.: 11895 Cov.: 23 AF XY: 0.549 AC XY: 17878 AN XY: 32573

African (AFR) AF: 0.569 AC: 17278 AN: 30345

American (AMR) AF: 0.630 AC: 6527 AN: 10358

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 1567 AN: 2615

East Asian (EAS) AF: 0.862 AC: 3027 AN: 3513

South Asian (SAS) AF: 0.567 AC: 1478 AN: 2605

European-Finnish (FIN) AF: 0.464 AC: 2698 AN: 5812

Middle Eastern (MID) AF: 0.529 AC: 110 AN: 208

European-Non Finnish (NFE) AF: 0.508 AC: 26747 AN: 52623

Other (OTH) AF: 0.570 AC: 853 AN: 1497

Alfa AF: 0.516 Hom.: 3728

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.28
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1993969; hg19: chrX-15208026;