X-137178554-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4 BS2

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 0.87 (30216 hom., 29443 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BS2: High Homozygotes in GnomAd at 30218 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.867 AC: 96381 AN: 111170 Hom.: 30218 Cov.: 24 AF XY: 0.878 AC XY: 29387 AN XY: 33486

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.895

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: 0.867 AC: 96430 AN: 111226 Hom.: 30216 Cov.: 24 AF XY: 0.878 AC XY: 29443 AN XY: 33550

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.986

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.897

Alfa AF: 0.969 Hom.: 115440

Bravo AF: 0.849

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
Cadd	Benign	21
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1334496; hg19: chrX-136260713;