rs9316529

Positions:

• chr13-51193305-T-C

Variant summary

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

The XR_001749988.2(LOC107984554):​n.37-1391A>G 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 0.0393 in 152,326 control chromosomes in the GnomAD database, including 311 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 0.039 (311 hom., cov: 32)
• Consequence: LOC107984554 XR_001749988.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984554	XR_001749988.2	n.37-1391A>G		intron_variant, non_coding_transcript_variant
LOC107984554	XR_007063803.1	n.37-1391A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C13orf42	ENST00000636098.1	n.206+6742A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5974 AN: 152208 Hom.: 308 Cov.: 32

Gnomad AFR AF: 0.00839

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0244

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0396

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

GnomAD4 genome AF: 0.0393 AC: 5993 AN: 152326 Hom.: 311 Cov.: 32 AF XY: 0.0419 AC XY: 3123 AN XY: 74484

Gnomad4 AFR AF: 0.00837

Gnomad4 AMR AF: 0.0894

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0244

Gnomad4 NFE AF: 0.0330

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0352 Hom.: 21

Bravo AF: 0.0441

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9316529; hg19: chr13-51767441;