rs5928363

Variant names:

• chrX-33765946-A-T
• rs5928363
• ENST00000439992.6:n.197+39311A>T

Variant summary

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

The ENST00000653446.1(ENSG00000233928):​n.185+39311A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 111,376 control chromosomes in the GnomAD database, including 1,146 homozygotes. There are 5,008 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 0.15 (1146 hom., 5008 hem., cov: 23)
• Consequence: ENSG00000233928 ENST00000653446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 publications found

Genes affected

ENSG00000233928 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233928	ENST00000439992.6	TSL:5	n.197+39311A>T		intron	N/A
	ENSG00000233928	ENST00000445233.2	TSL:5	n.114+23812A>T		intron	N/A
	ENSG00000233928	ENST00000653446.1		n.185+39311A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 16543 AN: 111321 Hom.: 1148 Cov.: 23

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.0259

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.148 AC: 16527 AN: 111376 Hom.: 1146 Cov.: 23 AF XY: 0.149 AC XY: 5008 AN XY: 33586

African (AFR) AF: 0.0289 AC: 890 AN: 30837

American (AMR) AF: 0.167 AC: 1744 AN: 10447

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 695 AN: 2633

East Asian (EAS) AF: 0.0257 AC: 91 AN: 3539

South Asian (SAS) AF: 0.182 AC: 483 AN: 2658

European-Finnish (FIN) AF: 0.293 AC: 1713 AN: 5852

Middle Eastern (MID) AF: 0.162 AC: 35 AN: 216

European-Non Finnish (NFE) AF: 0.200 AC: 10579 AN: 52989

Other (OTH) AF: 0.146 AC: 223 AN: 1526

Alfa AF: 0.178 Hom.: 1067

Bravo AF: 0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5928363;

hg19: chrX-33784063;