Genetic Variant C15orf32:n.277G>A (chr15-92472197-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000556865.1(C15orf32):n.277G>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
ENST00000556865.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.343

Publications

25 publications found

Variant links:

COSMIC-nc: COSV51572855

Genes affected

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

C15orf32 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.086).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C15orf32	NR_161370.1		n.521G>A		non_coding_transcript_exon	Exon 1 of 3
	C15orf32	NR_161371.1		n.521G>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C15orf32	ENST00000556865.1	TSL:1	n.277G>A		non_coding_transcript_exon	Exon 1 of 3
	C15orf32	ENST00000624458.1	TSL:1	n.544G>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56272

AN:

151848

Hom.:

10812

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.368

AC:

92171

AN:

250596

AF XY:

0.362

show subpopulations

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 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.:

AF XY:

0.315

AC XY:

189613

AN XY:

601802

show subpopulations

African (AFR)

AF:

0.450

AC:

11785

AN:

26208

American (AMR)

AF:

0.491

AC:

18248

AN:

37144

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

5417

AN:

16844

East Asian (EAS)

AF:

0.458

AC:

7686

AN:

16790

South Asian (SAS)

AF:

0.409

AC:

34032

AN:

83126

European-Finnish (FIN)

AF:

0.365

AC:

11894

AN:

32586

Middle Eastern (MID)

AF:

0.378

AC:

1689

AN:

4466

European-Non Finnish (NFE)

AF:

0.288

AC:

274638

AN:

953068

Other (OTH)

AF:

0.327

AC:

14362

AN:

43970

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

13633

27266

40900

54533

68166

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10642

21284

31926

42568

53210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.370

AC:

56294

AN:

151966

Hom.:

10817

Cov.:

AF XY:

0.378

AC XY:

28078

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.450

AC:

18668

AN:

41450

American (AMR)

AF:

0.426

AC:

6512

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

1071

AN:

3466

East Asian (EAS)

AF:

0.472

AC:

2423

AN:

5138

South Asian (SAS)

AF:

0.411

AC:

1971

AN:

4790

European-Finnish (FIN)

AF:

0.375

AC:

3963

AN:

10566

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.302

AC:

20534

AN:

67956

Other (OTH)

AF:

0.372

AC:

782

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1823

3647

5470

7294

9117

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.327

Hom.:

30959

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.22

(source)

DANN

Benign

0.90

PhyloP100

-0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over