chrX-30153744-C-T

Variant names:

• chrX-30153744-C-T
• rs5929069
• ENST00000796024.1:n.592-12747G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000796024.1(ENSG00000303603):​n.592-12747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0126 in 111,435 control chromosomes in the GnomAD database, including 11 homozygotes. There are 395 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 0.013 (11 hom., 395 hem., cov: 23)
• Consequence: ENSG00000303603 ENST00000796024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 0 publications found

Genes affected

ENSG00000303603 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0126 (1400/111435) while in subpopulation NFE AF = 0.0186 (987/53065). AF 95% confidence interval is 0.0176. There are 11 homozygotes in GnomAd4. There are 395 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 11 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796024.1. 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
	ENSG00000303603	ENST00000796024.1		n.592-12747G>A		intron	N/A
	ENSG00000303603	ENST00000796025.1		n.573-13846G>A		intron	N/A
	ENSG00000303603	ENST00000796026.1		n.564-12747G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0126 AC: 1400 AN: 111384 Hom.: 11 Cov.: 23

Gnomad AFR AF: 0.00255

Gnomad AMI AF: 0.0207

Gnomad AMR AF: 0.00592

Gnomad ASJ AF: 0.0151

Gnomad EAS AF: 0.000280

Gnomad SAS AF: 0.00271

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0140

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

GnomAD4 genome AF: 0.0126 AC: 1400 AN: 111435 Hom.: 11 Cov.: 23 AF XY: 0.0117 AC XY: 395 AN XY: 33637

African (AFR) AF: 0.00254 AC: 78 AN: 30681

American (AMR) AF: 0.00591 AC: 62 AN: 10483

Ashkenazi Jewish (ASJ) AF: 0.0151 AC: 40 AN: 2643

East Asian (EAS) AF: 0.000281 AC: 1 AN: 3565

South Asian (SAS) AF: 0.00272 AC: 7 AN: 2575

European-Finnish (FIN) AF: 0.0316 AC: 190 AN: 6014

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.0186 AC: 987 AN: 53065

Other (OTH) AF: 0.0139 AC: 21 AN: 1514

Alfa AF: 0.0159 Hom.: 366

Bravo AF: 0.0106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.46
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs5929069; hg19: chrX-30171861;