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).

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: 0.656 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 v4.3

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;