15-92472898-C-T

Variant names:

• chr15-92472898-C-T
• rs13380006
• ENST00000556865.1:n.603-55C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556865.1(C15orf32):​n.603-55C>T variant causes a intron 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 ENST00000556865.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556865.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C15orf32	NR_161370.1		n.847-55C>T		intron	N/A
	C15orf32	NR_161371.1		n.847-55C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C15orf32	ENST00000556865.1	TSL:1	n.603-55C>T		intron	N/A
	C15orf32	ENST00000624458.1	TSL:1	n.870-55C>T		intron	N/A

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

African (AFR) AF: 0.435 AC: 10793 AN: 24810

American (AMR) AF: 0.491 AC: 18114 AN: 36884

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 5213 AN: 16154

East Asian (EAS) AF: 0.456 AC: 7387 AN: 16194

South Asian (SAS) AF: 0.408 AC: 32819 AN: 80408

European-Finnish (FIN) AF: 0.364 AC: 11686 AN: 32142

Middle Eastern (MID) AF: 0.377 AC: 1629 AN: 4320

European-Non Finnish (NFE) AF: 0.288 AC: 257260 AN: 893494

Other (OTH) AF: 0.326 AC: 13554 AN: 41634

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

African (AFR) AF: 0.436 AC: 18082 AN: 41516

American (AMR) AF: 0.423 AC: 6477 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2428 AN: 5174

South Asian (SAS) AF: 0.411 AC: 1980 AN: 4820

European-Finnish (FIN) AF: 0.374 AC: 3956 AN: 10586

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20494 AN: 68006

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.338 Hom.: 1532

Bravo AF: 0.369

Asia WGS AF: 0.466 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.91
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13380006;

hg19: chr15-93016128;

COSMIC: COSV107269747;