rs4829605

chrX-137182822-C-AchrX-137182822-C-GchrX-137182822-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong 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 0.86 (30212 hom., 24310 hem., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd at 30216 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: 0.865 AC: 91061 AN: 105287 Hom.: 30216 Cov.: 19 AF XY: 0.867 AC XY: 24265 AN XY: 27987

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.961

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.891

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: 0.865 AC: 91096 AN: 105334 Hom.: 30212 Cov.: 19 AF XY: 0.867 AC XY: 24310 AN XY: 28044

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.986

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.892

Alfa AF: 0.945 Hom.: 20311

Bravo AF: 0.852

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.5
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4829605; hg19: chrX-136264981;