rs10492604

Variant names:

• chr13-58330179-T-C
• rs10492604
• ENST00000784591.1:n.369+10913T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000784591.1(ENSG00000302133):​n.369+10913T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,210 control chromosomes in the GnomAD database, including 1,806 homozygotes. 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 0.14 (1806 hom., cov: 32)
• Consequence: ENSG00000302133 ENST00000784591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 11 publications found

Genes affected

ENSG00000302133 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784591.1. 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
	ENSG00000302133	ENST00000784591.1		n.369+10913T>C		intron	N/A
	ENSG00000302133	ENST00000784592.1		n.318+10913T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21274 AN: 152092 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.140 AC: 21284 AN: 152210 Hom.: 1806 Cov.: 32 AF XY: 0.140 AC XY: 10400 AN XY: 74416

African (AFR) AF: 0.0631 AC: 2623 AN: 41562

American (AMR) AF: 0.211 AC: 3220 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3470

East Asian (EAS) AF: 0.0507 AC: 262 AN: 5172

South Asian (SAS) AF: 0.131 AC: 631 AN: 4828

European-Finnish (FIN) AF: 0.155 AC: 1645 AN: 10600

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11772 AN: 67978

Other (OTH) AF: 0.140 AC: 295 AN: 2114

Alfa AF: 0.160 Hom.: 9149

Bravo AF: 0.142

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	6.0
DANN	Benign	0.72
PhyloP100		-0.23

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: rs10492604;

hg19: chr13-58904313;