rs505971

Variant names:

• chrX-114580342-G-A
• rs505971

Your query was ambiguous. Multiple possible variants found:

• chrX-114580342-G-A
• chrX-114580342-G-C
• chrX-114580342-G-T

Variant summary

Our verdict is Likely benign. Variant got -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 0.65 (16483 hom., 19612 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.648 AC: 69977 AN: 108036 Hom.: 16490 Cov.: 21 AF XY: 0.643 AC XY: 19600 AN XY: 30466

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.676

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: 0.647 AC: 69976 AN: 108086 Hom.: 16483 Cov.: 21 AF XY: 0.642 AC XY: 19612 AN XY: 30526

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.677

Alfa AF: 0.478 Hom.: 2014

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs505971; hg19: chrX-113814808;