X-71200591-T-C

Variant names:

• chrX-71200591-T-C
• rs5980744

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 0.59 (13924 hom., 15876 hem., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75
• 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=-1.09).

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: 0.589 AC: 61030 AN: 103578 Hom.: 13913 Cov.: 19

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.631

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: 0.589 AC: 61052 AN: 103592 Hom.: 13924 Cov.: 19 AF XY: 0.592 AC XY: 15876 AN XY: 26810

African (AFR) AF: 0.753 AC: 21515 AN: 28578

American (AMR) AF: 0.632 AC: 5976 AN: 9460

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 1748 AN: 2563

East Asian (EAS) AF: 0.752 AC: 2425 AN: 3224

South Asian (SAS) AF: 0.622 AC: 1405 AN: 2259

European-Finnish (FIN) AF: 0.426 AC: 1954 AN: 4591

Middle Eastern (MID) AF: 0.700 AC: 133 AN: 190

European-Non Finnish (NFE) AF: 0.485 AC: 24571 AN: 50683

Other (OTH) AF: 0.637 AC: 887 AN: 1392

Alfa AF: 0.302 Hom.: 1201

Bravo AF: 0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.094
DANN	Benign	0.12
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs5980744; hg19: chrX-70420441;