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).

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: 0.553 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 v4.3

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;