rs7891451

Positions:

• chrX-71201173-A-G

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 0.60 (15354 hom., 18084 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

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: 0.603 AC: 65106 AN: 108051 Hom.: 15344 Cov.: 20 AF XY: 0.590 AC XY: 18035 AN XY: 30577

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.636

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: 0.603 AC: 65164 AN: 108098 Hom.: 15354 Cov.: 20 AF XY: 0.590 AC XY: 18084 AN XY: 30634

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.642

Alfa AF: 0.553 Hom.: 4184

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.9
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7891451; hg19: chrX-70421023;