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).

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: 0.517 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 v4.3

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;