X-118179210-C-T

Variant names:

• chrX-118179210-C-T
• rs1230828

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 0.73 (21386 hom., 23686 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.732 AC: 80993 AN: 110602 Hom.: 21389 Cov.: 23

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.852

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.728

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: 0.732 AC: 81025 AN: 110658 Hom.: 21386 Cov.: 23 AF XY: 0.720 AC XY: 23686 AN XY: 32890

African (AFR) AF: 0.724 AC: 22026 AN: 30439

American (AMR) AF: 0.616 AC: 6384 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2020 AN: 2633

East Asian (EAS) AF: 0.519 AC: 1822 AN: 3511

South Asian (SAS) AF: 0.508 AC: 1329 AN: 2618

European-Finnish (FIN) AF: 0.814 AC: 4724 AN: 5802

Middle Eastern (MID) AF: 0.843 AC: 182 AN: 216

European-Non Finnish (NFE) AF: 0.773 AC: 40894 AN: 52883

Other (OTH) AF: 0.725 AC: 1095 AN: 1511

Alfa AF: 0.740 Hom.: 19798

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.55
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1230828; hg19: chrX-117313173;