X-137178554-C-T

Variant names:

• chrX-137178554-C-T
• rs1334496

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

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 0.87 (30216 hom., 29443 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.867 AC: 96381 AN: 111170 Hom.: 30218 Cov.: 24

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.895

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: 0.867 AC: 96430 AN: 111226 Hom.: 30216 Cov.: 24 AF XY: 0.878 AC XY: 29443 AN XY: 33550

African (AFR) AF: 0.577 AC: 17590 AN: 30460

American (AMR) AF: 0.939 AC: 9894 AN: 10538

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 2584 AN: 2629

East Asian (EAS) AF: 0.927 AC: 3265 AN: 3521

South Asian (SAS) AF: 0.986 AC: 2609 AN: 2645

European-Finnish (FIN) AF: 0.997 AC: 6036 AN: 6052

Middle Eastern (MID) AF: 0.958 AC: 205 AN: 214

European-Non Finnish (NFE) AF: 0.986 AC: 52210 AN: 52974

Other (OTH) AF: 0.897 AC: 1354 AN: 1509

Alfa AF: 0.938 Hom.: 143959

Bravo AF: 0.849

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	21
DANN	Benign	0.71
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs1334496; hg19: chrX-136260713;