X-43614480-A-G

Variant names:

• chrX-43614480-A-G
• rs5906898

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 0.62 (15850 hom., 19763 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.621 AC: 68409 AN: 110133 Hom.: 15852 Cov.: 22

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.708

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.656

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: 0.621 AC: 68434 AN: 110187 Hom.: 15850 Cov.: 22 AF XY: 0.609 AC XY: 19763 AN XY: 32445

African (AFR) AF: 0.444 AC: 13460 AN: 30342

American (AMR) AF: 0.795 AC: 8164 AN: 10267

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 1820 AN: 2631

East Asian (EAS) AF: 0.534 AC: 1863 AN: 3491

South Asian (SAS) AF: 0.428 AC: 1118 AN: 2611

European-Finnish (FIN) AF: 0.562 AC: 3236 AN: 5760

Middle Eastern (MID) AF: 0.711 AC: 150 AN: 211

European-Non Finnish (NFE) AF: 0.706 AC: 37190 AN: 52697

Other (OTH) AF: 0.654 AC: 986 AN: 1508

Alfa AF: 0.653 Hom.: 13346

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs5906898; hg19: chrX-43473728;