rs5946504

Variant names:

• chrX-853815-C-T
• rs5946504

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.748 in 151,552 control chromosomes in the GnomAD database, including 43,275 homozygotes. There are 55,593 hemizygotes in GnomAD. 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 0.75 (43275 hom., 55593 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

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: 0.747 AC: 113196 AN: 151434 Hom.: 43230 Cov.: 29

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.727

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.748 AC: 113296 AN: 151552 Hom.: 43275 Cov.: 29 AF XY: 0.751 AC XY: 55593 AN XY: 74028

African (AFR) AF: 0.873 AC: 36133 AN: 41410

American (AMR) AF: 0.762 AC: 11593 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2019 AN: 3458

East Asian (EAS) AF: 0.995 AC: 5079 AN: 5102

South Asian (SAS) AF: 0.869 AC: 4170 AN: 4798

European-Finnish (FIN) AF: 0.667 AC: 7003 AN: 10496

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 45018 AN: 67786

Other (OTH) AF: 0.730 AC: 1533 AN: 2100

Bravo AF: 0.760

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs5946504; hg19: chrX-814550;