X-69585474-A-G

Variant names:

• chrX-69585474-A-G
• rs4844096

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 0.69 (19852 hom., 22024 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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: 0.689 AC: 75689 AN: 109927 Hom.: 19843 Cov.: 22

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.653

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: 0.689 AC: 75753 AN: 109971 Hom.: 19852 Cov.: 22 AF XY: 0.683 AC XY: 22024 AN XY: 32247

African (AFR) AF: 0.926 AC: 27966 AN: 30198

American (AMR) AF: 0.714 AC: 7390 AN: 10343

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1298 AN: 2626

East Asian (EAS) AF: 0.997 AC: 3503 AN: 3513

South Asian (SAS) AF: 0.735 AC: 1851 AN: 2517

European-Finnish (FIN) AF: 0.553 AC: 3158 AN: 5713

Middle Eastern (MID) AF: 0.451 AC: 96 AN: 213

European-Non Finnish (NFE) AF: 0.551 AC: 29048 AN: 52677

Other (OTH) AF: 0.658 AC: 987 AN: 1501

Alfa AF: 0.606 Hom.: 65350

Bravo AF: 0.714

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4844096; hg19: chrX-68805318;