rs5946342

Variant names:

• chrX-889941-T-C
• rs5946342

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.437 AC: 66363 AN: 151766 Hom.: 18403 Cov.: 31 AF XY: 0.446 AC XY: 33038 AN XY: 74086

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

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.404

Bravo AF: 0.461

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946342; hg19: chrX-850676;