chrX-103328477-T-C

Variant names:

• chrX-103328477-T-C
• rs5945971

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 0.67 (18704 hom., 21188 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• 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=-1.04).

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: 0.671 AC: 73563 AN: 109690 Hom.: 18701 Cov.: 22

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.552

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.644

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: 0.671 AC: 73614 AN: 109739 Hom.: 18704 Cov.: 22 AF XY: 0.661 AC XY: 21188 AN XY: 32051

African (AFR) AF: 0.911 AC: 27438 AN: 30108

American (AMR) AF: 0.621 AC: 6448 AN: 10386

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 1768 AN: 2615

East Asian (EAS) AF: 0.591 AC: 2040 AN: 3452

South Asian (SAS) AF: 0.752 AC: 1899 AN: 2525

European-Finnish (FIN) AF: 0.460 AC: 2618 AN: 5691

Middle Eastern (MID) AF: 0.550 AC: 116 AN: 211

European-Non Finnish (NFE) AF: 0.572 AC: 30089 AN: 52600

Other (OTH) AF: 0.644 AC: 955 AN: 1483

Alfa AF: 0.617 Hom.: 4848

Bravo AF: 0.692

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.53
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs5945971; hg19: chrX-102583405;