X-51483638-G-T

Variant names:

• chrX-51483638-G-T
• rs5987421

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 0.66 (17026 hom., 21741 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.659 AC: 72880 AN: 110665 Hom.: 17027 Cov.: 24

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.675

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: 0.658 AC: 72904 AN: 110719 Hom.: 17026 Cov.: 24 AF XY: 0.659 AC XY: 21741 AN XY: 32975

African (AFR) AF: 0.625 AC: 19041 AN: 30479

American (AMR) AF: 0.779 AC: 8159 AN: 10478

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 1989 AN: 2636

East Asian (EAS) AF: 0.923 AC: 3235 AN: 3503

South Asian (SAS) AF: 0.713 AC: 1850 AN: 2596

European-Finnish (FIN) AF: 0.577 AC: 3344 AN: 5792

Middle Eastern (MID) AF: 0.681 AC: 145 AN: 213

European-Non Finnish (NFE) AF: 0.638 AC: 33730 AN: 52849

Other (OTH) AF: 0.679 AC: 1021 AN: 1504

Alfa AF: 0.645 Hom.: 6112

Bravo AF: 0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.60
PhyloP100		0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5987421;

hg19: chrX-51226490;