chrX-95988788-T-C

Variant names:

• chrX-95988788-T-C
• rs4969656

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 0.82 (26667 hom., 26299 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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: 0.824 AC: 90339 AN: 109695 Hom.: 26677 Cov.: 22

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.819

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: 0.823 AC: 90354 AN: 109749 Hom.: 26667 Cov.: 22 AF XY: 0.820 AC XY: 26299 AN XY: 32061

African (AFR) AF: 0.759 AC: 22954 AN: 30236

American (AMR) AF: 0.867 AC: 8872 AN: 10231

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2212 AN: 2619

East Asian (EAS) AF: 0.491 AC: 1695 AN: 3453

South Asian (SAS) AF: 0.667 AC: 1725 AN: 2588

European-Finnish (FIN) AF: 0.900 AC: 5166 AN: 5737

Middle Eastern (MID) AF: 0.795 AC: 171 AN: 215

European-Non Finnish (NFE) AF: 0.873 AC: 45844 AN: 52511

Other (OTH) AF: 0.811 AC: 1209 AN: 1491

Alfa AF: 0.855 Hom.: 92384

Bravo AF: 0.818

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.45
DANN	Benign	0.30
PhyloP100		-1.0

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: rs4969656; hg19: chrX-95243787;