chrX-71201173-A-G

Variant names:

• chrX-71201173-A-G
• rs7891451

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.603 AC: 65106 AN: 108051 Hom.: 15344 Cov.: 20

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

African (AFR) AF: 0.825 AC: 24649 AN: 29885

American (AMR) AF: 0.633 AC: 6378 AN: 10068

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 1771 AN: 2600

East Asian (EAS) AF: 0.737 AC: 2402 AN: 3257

South Asian (SAS) AF: 0.586 AC: 1416 AN: 2418

European-Finnish (FIN) AF: 0.414 AC: 2282 AN: 5508

Middle Eastern (MID) AF: 0.689 AC: 146 AN: 212

European-Non Finnish (NFE) AF: 0.476 AC: 24732 AN: 52008

Other (OTH) AF: 0.642 AC: 959 AN: 1493

Alfa AF: 0.553 Hom.: 4184

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.9
DANN	Benign	0.17
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7891451; hg19: chrX-70421023;