rs929095

Variant names:

• chrX-43503701-C-G
• rs929095

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 0.55 (13206 hom., 18175 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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: 0.553 AC: 61080 AN: 110510 Hom.: 13210 Cov.: 23

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.569

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: 0.553 AC: 61093 AN: 110559 Hom.: 13206 Cov.: 23 AF XY: 0.553 AC XY: 18175 AN XY: 32839

African (AFR) AF: 0.267 AC: 8167 AN: 30544

American (AMR) AF: 0.696 AC: 7205 AN: 10348

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 1517 AN: 2620

East Asian (EAS) AF: 0.583 AC: 2019 AN: 3464

South Asian (SAS) AF: 0.451 AC: 1189 AN: 2636

European-Finnish (FIN) AF: 0.696 AC: 4025 AN: 5785

Middle Eastern (MID) AF: 0.637 AC: 137 AN: 215

European-Non Finnish (NFE) AF: 0.675 AC: 35626 AN: 52774

Other (OTH) AF: 0.568 AC: 855 AN: 1504

Alfa AF: 0.607 Hom.: 4712

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.67
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs929095; hg19: chrX-43362950; COSMIC: COSV68315919;