chrX-118179210-C-T

Variant names:

• chrX-118179210-C-T
• rs1230828

Variant summary

Our verdict is Likely benign. Variant got -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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

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: 0.732 AC: 80993 AN: 110602 Hom.: 21389 Cov.: 23 AF XY: 0.720 AC XY: 23644 AN XY: 32824

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

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.725

Alfa AF: 0.759 Hom.: 8136

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1230828; hg19: chrX-117313173;