rs932807

Variant names:

• chr13-51162719-T-C
• rs932807
• ENST00000433280.6:n.136+9534A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433280.6(C13orf42):​n.136+9534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,120 control chromosomes in the GnomAD database, including 4,065 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 0.21 (4065 hom., cov: 32)
• Consequence: C13orf42 ENST00000433280.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C13orf42	NR_102431.3	n.136+9534A>G		intron_variant	Intron 1 of 4
C13orf42	NR_102432.3	n.235+9269A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C13orf42	ENST00000433280.6	n.136+9534A>G		intron_variant	Intron 1 of 4	3
C13orf42	ENST00000569306.1	n.235+9269A>G		intron_variant	Intron 1 of 3	3
C13orf42	ENST00000636098.1	n.206+37328A>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32281 AN: 152002 Hom.: 4063 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.212 AC: 32276 AN: 152120 Hom.: 4065 Cov.: 32 AF XY: 0.212 AC XY: 15767 AN XY: 74378

Gnomad4 AFR AF: 0.0864

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.233

Alfa AF: 0.250 Hom.: 2281

Bravo AF: 0.211

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs932807; hg19: chr13-51736855; COSMIC: COSV67742932;