rs5946342

Positions:

• chrX-889941-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;