13-51165032-G-A

Variant names:

• chr13-51165032-G-A
• rs2408296
• ENST00000433280.6:n.136+7221C>T

Variant summary

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

The ENST00000433280.6(C13orf42):​n.136+7221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,016 control chromosomes in the GnomAD database, including 4,472 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 0.23 (4472 hom., cov: 32)
• Consequence: C13orf42 ENST00000433280.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 2 publications found

Genes affected

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 (AMR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433280.6. 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
	C13orf42	NR_102431.3		n.136+7221C>T		intron	N/A
	C13orf42	NR_102432.3		n.235+6956C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C13orf42	ENST00000433280.6	TSL:3	n.136+7221C>T		intron	N/A
	C13orf42	ENST00000569306.1	TSL:3	n.235+6956C>T		intron	N/A
	C13orf42	ENST00000636098.1	TSL:5	n.206+35015C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35262 AN: 151896 Hom.: 4467 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.232 AC: 35266 AN: 152016 Hom.: 4472 Cov.: 32 AF XY: 0.232 AC XY: 17247 AN XY: 74304

African (AFR) AF: 0.145 AC: 5995 AN: 41468

American (AMR) AF: 0.315 AC: 4815 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 730 AN: 3464

East Asian (EAS) AF: 0.0913 AC: 472 AN: 5170

South Asian (SAS) AF: 0.209 AC: 1005 AN: 4810

European-Finnish (FIN) AF: 0.268 AC: 2830 AN: 10554

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18651 AN: 67962

Other (OTH) AF: 0.243 AC: 513 AN: 2110

Alfa AF: 0.256 Hom.: 19928

Bravo AF: 0.234

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.64
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2408296; hg19: chr13-51739168; COSMIC: COSV67742952;