rs5946342

Variant names:

• chrX-889941-T-C
• rs5946342

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 0.438 in 151,884 control chromosomes in the GnomAD database, including 18,444 homozygotes. There are 33,146 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 0.44 (18444 hom., 33146 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 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: 0.437 AC: 66363 AN: 151766 Hom.: 18403 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.438 AC: 66457 AN: 151884 Hom.: 18444 Cov.: 31 AF XY: 0.447 AC XY: 33146 AN XY: 74214

African (AFR) AF: 0.737 AC: 30502 AN: 41414

American (AMR) AF: 0.441 AC: 6722 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4376 AN: 5160

South Asian (SAS) AF: 0.576 AC: 2763 AN: 4798

European-Finnish (FIN) AF: 0.326 AC: 3446 AN: 10556

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16198 AN: 67930

Other (OTH) AF: 0.404 AC: 853 AN: 2110

Bravo AF: 0.461

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.16
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs5946342; hg19: chrX-850676;