X-51544937-T-G

Variant names:

• chrX-51544937-T-G
• rs1541241

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 0.66 (17028 hom., 20914 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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: 0.656 AC: 72014 AN: 109757 Hom.: 17030 Cov.: 22

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.670

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: 0.656 AC: 72032 AN: 109812 Hom.: 17028 Cov.: 22 AF XY: 0.652 AC XY: 20914 AN XY: 32090

African (AFR) AF: 0.632 AC: 19064 AN: 30168

American (AMR) AF: 0.778 AC: 7931 AN: 10197

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 1973 AN: 2633

East Asian (EAS) AF: 0.925 AC: 3187 AN: 3446

South Asian (SAS) AF: 0.714 AC: 1804 AN: 2526

European-Finnish (FIN) AF: 0.554 AC: 3222 AN: 5817

Middle Eastern (MID) AF: 0.660 AC: 138 AN: 209

European-Non Finnish (NFE) AF: 0.633 AC: 33315 AN: 52648

Other (OTH) AF: 0.674 AC: 1004 AN: 1490

Alfa AF: 0.645 Hom.: 18255

Bravo AF: 0.677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.63
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1541241; hg19: chrX-51287789;