chr13-51190901-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984554	XR_001749988.2	n.462T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107984554	XR_007063803.1	n.1050T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307205	ENST00000824523.1	n.541T>C		non_coding_transcript_exon_variant	Exon 3 of 3
C13orf42	ENST00000636098.1	n.206+9146T>C		intron_variant	Intron 1 of 4	5

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 v4.3

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;