rs5946331

Variant names:

• chrX-854266-A-G
• rs5946331

Your query was ambiguous. Multiple possible variants found:

• chrX-854266-A-G
• chrX-854266-A-T

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 0.657 in 151,130 control chromosomes in the GnomAD database, including 33,796 homozygotes. There are 48,688 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 0.66 (33796 hom., 48688 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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: 0.657 AC: 99267 AN: 151010 Hom.: 33760 Cov.: 29

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.657 AC: 99362 AN: 151130 Hom.: 33796 Cov.: 29 AF XY: 0.659 AC XY: 48688 AN XY: 73830

African (AFR) AF: 0.817 AC: 33765 AN: 41326

American (AMR) AF: 0.658 AC: 9985 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1491 AN: 3446

East Asian (EAS) AF: 0.929 AC: 4739 AN: 5102

South Asian (SAS) AF: 0.733 AC: 3501 AN: 4774

European-Finnish (FIN) AF: 0.565 AC: 5927 AN: 10490

Middle Eastern (MID) AF: 0.600 AC: 174 AN: 290

European-Non Finnish (NFE) AF: 0.562 AC: 37950 AN: 67530

Other (OTH) AF: 0.622 AC: 1303 AN: 2094

Bravo AF: 0.668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.035
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs5946331; hg19: chrX-815001;