15-92472898-C-T

Variant summary

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

The NR_161371.1(C15orf32):n.847-55C>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 0.319 in 1,298,224 control chromosomes in the GnomAD database, including 68,536 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 0.37 (10528 hom., cov: 33)
  • Exomes 𝑓: 0.31 (58008 hom.)
• Consequence: C15orf32 NR_161371.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C15orf32	NR_161371.1	n.847-55C>T		intron_variant, non_coding_transcript_variant
C15orf32	NR_161370.1	n.847-55C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C15orf32	ENST00000556865.1	n.603-55C>T		intron_variant, non_coding_transcript_variant		1
C15orf32	ENST00000624458.1	n.870-55C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55612 AN: 152066 Hom.: 10522 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.368

GnomAD4 exome AF: 0.313 AC: 358455 AN: 1146040 Hom.: 58008 AF XY: 0.315 AC XY: 179024 AN XY: 567810

Gnomad4 AFR exome AF: 0.435

Gnomad4 AMR exome AF: 0.491

Gnomad4 ASJ exome AF: 0.323

Gnomad4 EAS exome AF: 0.456

Gnomad4 SAS exome AF: 0.408

Gnomad4 FIN exome AF: 0.364

Gnomad4 NFE exome AF: 0.288

Gnomad4 OTH exome AF: 0.326

GnomAD4 genome AF: 0.366 AC: 55636 AN: 152184 Hom.: 10528 Cov.: 33 AF XY: 0.373 AC XY: 27789 AN XY: 74402

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.366

Alfa AF: 0.336 Hom.: 1462

Bravo AF: 0.369

Asia WGS AF: 0.466 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.5
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13380006; hg19: chr15-93016128;