rs4269695

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).

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: 0.922 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 v4.3

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;