chrX-51667658-G-A

Variant names:

• chrX-51667658-G-A
• rs4473816

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 0.74 (21638 hom., 24050 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934
• 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=-1.06).

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: 0.743 AC: 81653 AN: 109864 Hom.: 21636 Cov.: 23

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.749

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: 0.743 AC: 81692 AN: 109899 Hom.: 21638 Cov.: 23 AF XY: 0.746 AC XY: 24050 AN XY: 32259

African (AFR) AF: 0.820 AC: 24816 AN: 30278

American (AMR) AF: 0.820 AC: 8479 AN: 10337

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2059 AN: 2634

East Asian (EAS) AF: 0.926 AC: 3250 AN: 3508

South Asian (SAS) AF: 0.762 AC: 2014 AN: 2644

European-Finnish (FIN) AF: 0.610 AC: 3266 AN: 5352

Middle Eastern (MID) AF: 0.692 AC: 146 AN: 211

European-Non Finnish (NFE) AF: 0.682 AC: 35984 AN: 52762

Other (OTH) AF: 0.752 AC: 1125 AN: 1497

Alfa AF: 0.676 Hom.: 17280

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.16
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs4473816; hg19: chrX-51410590;