chrX-84961591-A-G

Variant names:

• chrX-84961591-A-G
• rs489404

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 0.77 (23545 hom., 25309 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• 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=-0.94).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.770 AC: 85079 AN: 110478 Hom.: 23545 Cov.: 23

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.773

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: 0.770 AC: 85138 AN: 110527 Hom.: 23545 Cov.: 23 AF XY: 0.773 AC XY: 25309 AN XY: 32755

African (AFR) AF: 0.946 AC: 28899 AN: 30537

American (AMR) AF: 0.744 AC: 7680 AN: 10318

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 1990 AN: 2627

East Asian (EAS) AF: 0.673 AC: 2342 AN: 3482

South Asian (SAS) AF: 0.851 AC: 2235 AN: 2627

European-Finnish (FIN) AF: 0.735 AC: 4271 AN: 5810

Middle Eastern (MID) AF: 0.819 AC: 172 AN: 210

European-Non Finnish (NFE) AF: 0.682 AC: 35993 AN: 52741

Other (OTH) AF: 0.771 AC: 1157 AN: 1501

Alfa AF: 0.725 Hom.: 6478

Bravo AF: 0.775

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs489404; hg19: chrX-84216597;