rs5905587

Variant names:

• chrX-43974750-T-C
• rs5905587

Your query was ambiguous. Multiple possible variants found:

• chrX-43974750-T-C
• chrX-43974750-T-G

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 0.60 (14669 hom., 18715 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• 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=-0.92).

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: 0.603 AC: 65882 AN: 109319 Hom.: 14662 Cov.: 22

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.581

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: 0.603 AC: 65926 AN: 109367 Hom.: 14669 Cov.: 22 AF XY: 0.591 AC XY: 18715 AN XY: 31675

African (AFR) AF: 0.629 AC: 18888 AN: 30010

American (AMR) AF: 0.526 AC: 5379 AN: 10217

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 1614 AN: 2610

East Asian (EAS) AF: 0.334 AC: 1163 AN: 3480

South Asian (SAS) AF: 0.339 AC: 863 AN: 2543

European-Finnish (FIN) AF: 0.660 AC: 3654 AN: 5540

Middle Eastern (MID) AF: 0.481 AC: 102 AN: 212

European-Non Finnish (NFE) AF: 0.627 AC: 32995 AN: 52598

Other (OTH) AF: 0.576 AC: 856 AN: 1485

Alfa AF: 0.614 Hom.: 86774

Bravo AF: 0.600

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.69
DANN	Benign	0.34
PhyloP100		-1.3

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: rs5905587;

hg19: chrX-43833996;