X-93658167-T-C

Variant names:

• chrX-93658167-T-C
• rs4893039

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 0.52 (11023 hom., 16179 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

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: 0.525 AC: 57119 AN: 108880 Hom.: 11014 Cov.: 21

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.511

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: 0.525 AC: 57179 AN: 108937 Hom.: 11023 Cov.: 21 AF XY: 0.517 AC XY: 16179 AN XY: 31323

African (AFR) AF: 0.624 AC: 18674 AN: 29909

American (AMR) AF: 0.542 AC: 5477 AN: 10097

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1309 AN: 2618

East Asian (EAS) AF: 0.425 AC: 1458 AN: 3430

South Asian (SAS) AF: 0.508 AC: 1275 AN: 2509

European-Finnish (FIN) AF: 0.515 AC: 2888 AN: 5608

Middle Eastern (MID) AF: 0.488 AC: 103 AN: 211

European-Non Finnish (NFE) AF: 0.477 AC: 25017 AN: 52393

Other (OTH) AF: 0.510 AC: 757 AN: 1485

Alfa AF: 0.452 Hom.: 9782

Bravo AF: 0.534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.37
PhyloP100		-2.1

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: rs4893039;

hg19: chrX-92913166;