rs938059

Variant names:

• chrX-67116885-C-A
• rs938059

Your query was ambiguous. Multiple possible variants found:

• chrX-67116885-C-A
• chrX-67116885-C-G
• chrX-67116885-C-T

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 0.66 (20461 hom., 21450 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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: 0.658 AC: 72231 AN: 109841 Hom.: 20468 Cov.: 22

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.698

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: 0.657 AC: 72223 AN: 109892 Hom.: 20461 Cov.: 22 AF XY: 0.667 AC XY: 21450 AN XY: 32144

African (AFR) AF: 0.155 AC: 4727 AN: 30427

American (AMR) AF: 0.831 AC: 8496 AN: 10229

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 2416 AN: 2630

East Asian (EAS) AF: 0.998 AC: 3427 AN: 3433

South Asian (SAS) AF: 0.918 AC: 2288 AN: 2492

European-Finnish (FIN) AF: 0.831 AC: 4774 AN: 5747

Middle Eastern (MID) AF: 0.756 AC: 161 AN: 213

European-Non Finnish (NFE) AF: 0.843 AC: 44292 AN: 52552

Other (OTH) AF: 0.700 AC: 1045 AN: 1493

Alfa AF: 0.796 Hom.: 50192

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.27
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs938059; hg19: chrX-66336727;