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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs4893039; hg19: chrX-92913166;