chrX-71322321-C-T

Variant names:

• chrX-71322321-C-T
• rs4269695

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 0.92 (33165 hom., 28827 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• 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=-0.91).

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: 0.922 AC: 100482 AN: 108987 Hom.: 33169 Cov.: 21

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.923

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.942

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: 0.922 AC: 100531 AN: 109041 Hom.: 33165 Cov.: 21 AF XY: 0.922 AC XY: 28827 AN XY: 31277

African (AFR) AF: 0.982 AC: 29430 AN: 29979

American (AMR) AF: 0.955 AC: 9563 AN: 10012

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2210 AN: 2613

East Asian (EAS) AF: 0.999 AC: 3501 AN: 3504

South Asian (SAS) AF: 0.888 AC: 2229 AN: 2511

European-Finnish (FIN) AF: 0.925 AC: 5193 AN: 5615

Middle Eastern (MID) AF: 0.925 AC: 198 AN: 214

European-Non Finnish (NFE) AF: 0.881 AC: 46234 AN: 52450

Other (OTH) AF: 0.943 AC: 1392 AN: 1476

Alfa AF: 0.895 Hom.: 7931

Bravo AF: 0.932

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.44
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4269695; hg19: chrX-70542171;