rs8040009

Positions:

• chr15-92501109-T-C
• chr15-92501109-T-G

Variant summary

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

The NR_161371.1(C15orf32):​n.1756T>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 0.302 in 152,106 control chromosomes in the GnomAD database, including 9,895 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 0.30 (9895 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: C15orf32 NR_161371.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

C15orf32 (HGNC:26549): (chromosome 15 putative open reading frame 32)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C15orf32	NR_161371.1	n.1756T>C		non_coding_transcript_exon_variant	3/3
C15orf32	NR_161370.1	n.1718T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C15orf32	ENST00000624458.1	n.1741T>C		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45850 AN: 151988 Hom.: 9883 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.277

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.302 AC: 45905 AN: 152106 Hom.: 9895 Cov.: 32 AF XY: 0.295 AC XY: 21904 AN XY: 74358

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.278

Alfa AF: 0.186 Hom.: 5076

Bravo AF: 0.321

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8040009; hg19: chr15-93044339;