13-51190901-A-G

Position:

• chr13-51190901-A-G

Variant summary

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

The XR_001749988.2(LOC107984554):​n.462T>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: LOC107984554 XR_001749988.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

LOC107984554 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984554	XR_001749988.2	n.462T>C		non_coding_transcript_exon_variant	3/3
LOC107984554	XR_007063803.1	n.1050T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C13orf42	ENST00000636098.1	n.206+9146T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.00853

Gnomad4 AMR AF: 0.0891

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0243

Gnomad4 NFE AF: 0.0329

Gnomad4 OTH AF: 0.0418

Alfa AF: 0.0395 Hom.: 78

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492518; hg19: chr13-51765037;