X-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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;