rs5934349

Variant names:

• chrX-8042359-A-G
• rs5934349
• ENST00000659022.1:n.971+112946A>G

Variant summary

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

The ENST00000659022.1(ENSG00000285679):​n.971+112946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 111,316 control chromosomes in the GnomAD database, including 2,666 homozygotes. There are 7,604 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 0.25 (2666 hom., 7604 hem., cov: 23)
• Consequence: ENSG00000285679 ENST00000659022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 0 publications found

Genes affected

ENSG00000285679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659022.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000285679	ENST00000659022.1		n.971+112946A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.246 AC: 27323 AN: 111268 Hom.: 2667 Cov.: 23

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.270

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.246 AC: 27355 AN: 111316 Hom.: 2666 Cov.: 23 AF XY: 0.226 AC XY: 7604 AN XY: 33600

African (AFR) AF: 0.317 AC: 9696 AN: 30557

American (AMR) AF: 0.163 AC: 1720 AN: 10535

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 804 AN: 2642

East Asian (EAS) AF: 0.0719 AC: 254 AN: 3531

South Asian (SAS) AF: 0.0849 AC: 228 AN: 2687

European-Finnish (FIN) AF: 0.173 AC: 1043 AN: 6038

Middle Eastern (MID) AF: 0.288 AC: 61 AN: 212

European-Non Finnish (NFE) AF: 0.247 AC: 13086 AN: 52927

Other (OTH) AF: 0.238 AC: 358 AN: 1507

Alfa AF: 0.254 Hom.: 2039

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.65
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs5934349; hg19: chrX-8010400;