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).

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: 0.603 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 v4.3

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;