rs3125945

Variant names:

• chrX-71038886-A-G
• rs3125945

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 0.63 (16615 hom., 20208 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 4 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.632 AC: 69705 AN: 110347 Hom.: 16609 Cov.: 22

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.636

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: 0.632 AC: 69755 AN: 110398 Hom.: 16615 Cov.: 22 AF XY: 0.619 AC XY: 20208 AN XY: 32646

African (AFR) AF: 0.835 AC: 25301 AN: 30303

American (AMR) AF: 0.659 AC: 6775 AN: 10282

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 1565 AN: 2633

East Asian (EAS) AF: 0.394 AC: 1370 AN: 3476

South Asian (SAS) AF: 0.459 AC: 1218 AN: 2653

European-Finnish (FIN) AF: 0.462 AC: 2703 AN: 5849

Middle Eastern (MID) AF: 0.634 AC: 135 AN: 213

European-Non Finnish (NFE) AF: 0.552 AC: 29141 AN: 52800

Other (OTH) AF: 0.642 AC: 974 AN: 1517

Alfa AF: 0.586 Hom.: 56824

Bravo AF: 0.656

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.89
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3125945; hg19: chrX-70258736;