X-67116885-C-A

Variant names:

• chrX-67116885-C-A
• rs938059

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).

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: 0.658 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 v4.3

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;