rs1541238

Variant names:

• chrX-51600783-G-C
• rs1541238

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 0.70 (19244 hom., 22865 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 4 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: 0.697 AC: 77110 AN: 110657 Hom.: 19240 Cov.: 23

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.700

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: 0.697 AC: 77158 AN: 110707 Hom.: 19244 Cov.: 23 AF XY: 0.694 AC XY: 22865 AN XY: 32943

African (AFR) AF: 0.746 AC: 22717 AN: 30451

American (AMR) AF: 0.798 AC: 8338 AN: 10455

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2005 AN: 2644

East Asian (EAS) AF: 0.923 AC: 3224 AN: 3494

South Asian (SAS) AF: 0.724 AC: 1879 AN: 2595

European-Finnish (FIN) AF: 0.561 AC: 3270 AN: 5826

Middle Eastern (MID) AF: 0.662 AC: 141 AN: 213

European-Non Finnish (NFE) AF: 0.646 AC: 34139 AN: 52851

Other (OTH) AF: 0.703 AC: 1060 AN: 1508

Alfa AF: 0.669 Hom.: 5248

Bravo AF: 0.719

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.53
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs1541238; hg19: chrX-51343635;