rs2408296

Positions:

• chr13-51165032-G-A
• chr13-51165032-G-C

Variant summary

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

The NR_102431.3(C13orf42):​n.136+7221C>T variant causes a intron, non coding transcript 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 NR_102431.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C13orf42	NR_102431.3	n.136+7221C>T		intron_variant, non_coding_transcript_variant
C13orf42	NR_102432.3	n.235+6956C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C13orf42	ENST00000433280.6	n.136+7221C>T		intron_variant, non_coding_transcript_variant		3
C13orf42	ENST00000569306.1	n.235+6956C>T		intron_variant, non_coding_transcript_variant		3
C13orf42	ENST00000636098.1	n.206+35015C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0913

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.243

Alfa AF: 0.260 Hom.: 8415

Bravo AF: 0.234

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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