rs4570308

Variant names:

• chrX-43652249-G-A
• rs4570308

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 0.60 (14924 hom., 19281 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.603 AC: 66423 AN: 110074 Hom.: 14931 Cov.: 22

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.618

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: 0.603 AC: 66430 AN: 110129 Hom.: 14924 Cov.: 22 AF XY: 0.594 AC XY: 19281 AN XY: 32453

African (AFR) AF: 0.442 AC: 13363 AN: 30228

American (AMR) AF: 0.664 AC: 6827 AN: 10284

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 1788 AN: 2631

East Asian (EAS) AF: 0.423 AC: 1464 AN: 3461

South Asian (SAS) AF: 0.384 AC: 999 AN: 2600

European-Finnish (FIN) AF: 0.567 AC: 3271 AN: 5765

Middle Eastern (MID) AF: 0.689 AC: 146 AN: 212

European-Non Finnish (NFE) AF: 0.705 AC: 37193 AN: 52766

Other (OTH) AF: 0.616 AC: 929 AN: 1509

Alfa AF: 0.647 Hom.: 5051

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4570308; hg19: chrX-43511497;