chrX-121839996-A-G

Variant names:

• chrX-121839996-A-G
• rs4509467

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 0.75 (22274 hom., 24679 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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: 0.749 AC: 82751 AN: 110488 Hom.: 22281 Cov.: 23

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.584

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.707

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: 0.749 AC: 82788 AN: 110539 Hom.: 22274 Cov.: 23 AF XY: 0.752 AC XY: 24679 AN XY: 32803

African (AFR) AF: 0.899 AC: 27413 AN: 30506

American (AMR) AF: 0.778 AC: 8047 AN: 10347

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1470 AN: 2619

East Asian (EAS) AF: 0.969 AC: 3406 AN: 3514

South Asian (SAS) AF: 0.683 AC: 1822 AN: 2667

European-Finnish (FIN) AF: 0.729 AC: 4235 AN: 5812

Middle Eastern (MID) AF: 0.575 AC: 122 AN: 212

European-Non Finnish (NFE) AF: 0.660 AC: 34796 AN: 52703

Other (OTH) AF: 0.701 AC: 1041 AN: 1485

Alfa AF: 0.590 Hom.: 4166

Bravo AF: 0.763

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.29
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4509467; hg19: chrX-120973849;