rs4456006

Variant names:

• chrX-67808380-C-A
• rs4456006

Your query was ambiguous. Multiple possible variants found:

• chrX-67808380-C-A
• chrX-67808380-C-G
• chrX-67808380-C-T

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 0.64 (18647 hom., 21855 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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: 0.642 AC: 71246 AN: 110968 Hom.: 18656 Cov.: 23

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.669

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: 0.642 AC: 71257 AN: 111025 Hom.: 18647 Cov.: 23 AF XY: 0.657 AC XY: 21855 AN XY: 33283

African (AFR) AF: 0.204 AC: 6261 AN: 30667

American (AMR) AF: 0.795 AC: 8302 AN: 10446

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2117 AN: 2641

East Asian (EAS) AF: 0.998 AC: 3473 AN: 3480

South Asian (SAS) AF: 0.902 AC: 2347 AN: 2602

European-Finnish (FIN) AF: 0.824 AC: 4852 AN: 5886

Middle Eastern (MID) AF: 0.650 AC: 139 AN: 214

European-Non Finnish (NFE) AF: 0.797 AC: 42150 AN: 52891

Other (OTH) AF: 0.673 AC: 1020 AN: 1516

Alfa AF: 0.748 Hom.: 91268

Bravo AF: 0.627

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4456006; hg19: chrX-67028222;