rs1202918

Variant names:

• chrX-151271258-T-A
• rs1202918

Your query was ambiguous. Multiple possible variants found:

• chrX-151271258-T-A
• chrX-151271258-T-C

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 0.52 (10794 hom., 16312 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.517 AC: 56993 AN: 110304 Hom.: 10789 Cov.: 22

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.422

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.496

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: 0.517 AC: 57022 AN: 110353 Hom.: 10794 Cov.: 22 AF XY: 0.500 AC XY: 16312 AN XY: 32631

African (AFR) AF: 0.594 AC: 18031 AN: 30360

American (AMR) AF: 0.443 AC: 4610 AN: 10397

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1293 AN: 2642

East Asian (EAS) AF: 0.593 AC: 2028 AN: 3420

South Asian (SAS) AF: 0.396 AC: 1015 AN: 2560

European-Finnish (FIN) AF: 0.444 AC: 2624 AN: 5907

Middle Eastern (MID) AF: 0.417 AC: 88 AN: 211

European-Non Finnish (NFE) AF: 0.497 AC: 26190 AN: 52691

Other (OTH) AF: 0.500 AC: 747 AN: 1495

Alfa AF: 0.497 Hom.: 3557

Bravo AF: 0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
DANN	Benign	0.79
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1202918; hg19: chrX-150439730;