chrX-71200591-T-C

Position:

• chrX-71200591-T-C

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 0.59 (13924 hom., 15876 hem., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.589 AC: 61030 AN: 103578 Hom.: 13913 Cov.: 19 AF XY: 0.592 AC XY: 15864 AN XY: 26786

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.631

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: 0.589 AC: 61052 AN: 103592 Hom.: 13924 Cov.: 19 AF XY: 0.592 AC XY: 15876 AN XY: 26810

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.637

Alfa AF: 0.302 Hom.: 1201

Bravo AF: 0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.094
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5980744; hg19: chrX-70420441;