dbSNP rs1455773: 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C15orf32	NR_161370.1 link	n.521G>A		non_coding_transcript_exon_variant	Exon 1 of 3
C15orf32	NR_161371.1 link	n.521G>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C15orf32	ENST00000556865.1 link	n.277G>A		non_coding_transcript_exon_variant	Exon 1 of 3	1
C15orf32	ENST00000624458.1 link	n.544G>A		non_coding_transcript_exon_variant	Exon 1 of 3	1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over