15-92472197-G-A

Position:

• chr15-92472197-G-A

Variant summary

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

The NR_161371.1(C15orf32):​n.521G>A 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 0.319 in 1,366,168 control chromosomes in the GnomAD database, including 72,282 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 (10817 hom., cov: 32)
  • Exomes 𝑓: 0.31 (61465 hom.)
• Consequence: C15orf32 NR_161371.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

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 = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C15orf32	NR_161371.1	n.521G>A		non_coding_transcript_exon_variant	1/3
C15orf32	NR_161370.1	n.521G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C15orf32	ENST00000556865.1	n.277G>A		non_coding_transcript_exon_variant	1/3	1
C15orf32	ENST00000624458.1	n.544G>A		non_coding_transcript_exon_variant	1/3	1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56272 AN: 151848 Hom.: 10812 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.374

GnomAD3 exomes AF: 0.368 AC: 92171 AN: 250596 Hom.: 17822 AF XY: 0.362 AC XY: 49053 AN XY: 135464

Gnomad AFR exome AF: 0.447

Gnomad AMR exome AF: 0.491

Gnomad ASJ exome AF: 0.315

Gnomad EAS exome AF: 0.454

Gnomad SAS exome AF: 0.410

Gnomad FIN exome AF: 0.369

Gnomad NFE exome AF: 0.299

Gnomad OTH exome AF: 0.359

GnomAD4 exome AF: 0.313 AC: 379751 AN: 1214202 Hom.: 61465 Cov.: 33 AF XY: 0.315 AC XY: 189613 AN XY: 601802

Gnomad4 AFR exome AF: 0.450

Gnomad4 AMR exome AF: 0.491

Gnomad4 ASJ exome AF: 0.322

Gnomad4 EAS exome AF: 0.458

Gnomad4 SAS exome AF: 0.409

Gnomad4 FIN exome AF: 0.365

Gnomad4 NFE exome AF: 0.288

Gnomad4 OTH exome AF: 0.327

GnomAD4 genome AF: 0.370 AC: 56294 AN: 151966 Hom.: 10817 Cov.: 32 AF XY: 0.378 AC XY: 28078 AN XY: 74246

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.372

Alfa AF: 0.317 Hom.: 18843

Bravo AF: 0.375

Asia WGS AF: 0.470 AC: 1635 AN: 3478

EpiCase AF: 0.304

EpiControl AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.22
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455773; hg19: chr15-93015427; COSMIC: COSV51572855;