rs10492518

Variant names:

• chr13-51190901-A-G
• rs10492518
• ENST00000824523.1:n.541T>C

Variant summary

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

The ENST00000824523.1(ENSG00000307205):​n.541T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 150,772 control chromosomes in the GnomAD database, including 313 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 0.040 (313 hom., cov: 32)
• Consequence: ENSG00000307205 ENST00000824523.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

Genes affected

ENSG00000307205 (HGNC:):

C13orf42 (HGNC:42693): (chromosome 13 open reading frame 42)

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 (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824523.1. 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
	ENSG00000307205	ENST00000824523.1		n.541T>C		non_coding_transcript_exon	Exon 3 of 3
	C13orf42	ENST00000636098.1	TSL:5	n.206+9146T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0396 AC: 5973 AN: 150658 Hom.: 310 Cov.: 32

Gnomad AFR AF: 0.00855

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0243

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0399

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

GnomAD4 genome AF: 0.0397 AC: 5992 AN: 150772 Hom.: 313 Cov.: 32 AF XY: 0.0424 AC XY: 3124 AN XY: 73728

African (AFR) AF: 0.00853 AC: 342 AN: 40096

American (AMR) AF: 0.0891 AC: 1361 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1296 AN: 5170

South Asian (SAS) AF: 0.0416 AC: 201 AN: 4826

European-Finnish (FIN) AF: 0.0243 AC: 258 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0329 AC: 2237 AN: 68026

Other (OTH) AF: 0.0418 AC: 88 AN: 2104

Alfa AF: 0.0381 Hom.: 85

Bravo AF: 0.0440

Asia WGS AF: 0.110 AC: 379 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.31
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10492518; hg19: chr13-51765037;