13-51150528-T-C

Variant names:

• chr13-51150528-T-C
• rs7325564
• ENST00000433280.6:n.136+21725A>G

Variant summary

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

The ENST00000433280.6(C13orf42):​n.136+21725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,160 control chromosomes in the GnomAD database, including 32,744 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 0.64 (32744 hom., cov: 32)
• Consequence: C13orf42 ENST00000433280.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C13orf42	NR_102431.3		n.136+21725A>G		intron	N/A
	C13orf42	NR_102432.3		n.235+21460A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C13orf42	ENST00000433280.6	TSL:3	n.136+21725A>G		intron	N/A
	C13orf42	ENST00000569306.1	TSL:3	n.235+21460A>G		intron	N/A
	C13orf42	ENST00000636098.1	TSL:5	n.207-37306A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97357 AN: 152042 Hom.: 32732 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.640 AC: 97400 AN: 152160 Hom.: 32744 Cov.: 32 AF XY: 0.649 AC XY: 48248 AN XY: 74380

African (AFR) AF: 0.429 AC: 17800 AN: 41498

American (AMR) AF: 0.605 AC: 9251 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2499 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4383 AN: 5184

South Asian (SAS) AF: 0.725 AC: 3494 AN: 4820

European-Finnish (FIN) AF: 0.834 AC: 8841 AN: 10596

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48850 AN: 67994

Other (OTH) AF: 0.642 AC: 1355 AN: 2112

Alfa AF: 0.684 Hom.: 116034

Bravo AF: 0.614

Asia WGS AF: 0.747 AC: 2595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.2
DANN	Benign	0.82
PhyloP100		0.82

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: rs7325564;

hg19: chr13-51724664;