X-114580342-G-A

Variant names:

• chrX-114580342-G-A
• rs505971

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 0.65 (16483 hom., 19612 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 3 publications found

ACMG classification

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

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

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: 0.648 AC: 69977 AN: 108036 Hom.: 16490 Cov.: 21

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

African (AFR) AF: 0.593 AC: 17593 AN: 29669

American (AMR) AF: 0.642 AC: 6450 AN: 10053

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 1643 AN: 2614

East Asian (EAS) AF: 0.832 AC: 2835 AN: 3406

South Asian (SAS) AF: 0.616 AC: 1508 AN: 2447

European-Finnish (FIN) AF: 0.720 AC: 3889 AN: 5398

Middle Eastern (MID) AF: 0.612 AC: 131 AN: 214

European-Non Finnish (NFE) AF: 0.660 AC: 34406 AN: 52148

Other (OTH) AF: 0.677 AC: 992 AN: 1465

Alfa AF: 0.478 Hom.: 2014

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs505971; hg19: chrX-113814808;