dbSNP rs3132449: C6orf47:c.*827G>A (chr6-31658236-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021184.4(C6orf47):c.*827G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 905,250 control chromosomes in the GnomAD database, including 4,622 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 0.073 ( 531 hom., cov: 32)

Exomes 𝑓: 0.088 ( 4091 hom. )

Consequence

C6orf47
NM_021184.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.119

Publications

16 publications found

Variant links:

Genes affected

C6orf47 (HGNC:19076): (chromosome 6 open reading frame 47)

C6orf47 links:

APOM (HGNC:13916): (apolipoprotein M) The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Alternate splicing results in both coding and non-coding variants of this gene. [provided by RefSeq, Jan 2012]

APOM links:

C6orf47-AS1 (HGNC:39767): (C6orf47 antisense RNA 1)

C6orf47-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf47	NM_021184.4 link	c.*827G>A		downstream_gene_variant		ENST00000375911.2	NP_067007.3
APOM	NM_019101.3 link	c.*147C>T		downstream_gene_variant		ENST00000375916.4	NP_061974.2	O95445-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf47	ENST00000375911.2 link	c.*827G>A		downstream_gene_variant		6	NM_021184.4	ENSP00000365076.1		O95873
APOM	ENST00000375916.4 link	c.*147C>T		downstream_gene_variant		1	NM_019101.3	ENSP00000365081.3		O95445-1

Frequencies

GnomAD3 genomes

AF:

0.0726

AC:

11047

AN:

152108

Hom.:

531

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0487

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.0356

Gnomad ASJ

AF:

0.0398

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.0786

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.0555

GnomAD4 exome

AF:

0.0879

AC:

66190

AN:

753024

Hom.:

4091

Cov.:

AF XY:

0.0841

AC XY:

33024

AN XY:

392450

show subpopulations

African (AFR)

AF:

0.0495

AC:

958

AN:

19340

American (AMR)

AF:

0.0265

AC:

859

AN:

32464

Ashkenazi Jewish (ASJ)

AF:

0.0414

AC:

772

AN:

18646

East Asian (EAS)

AF:

0.000113

AC:

AN:

35314

South Asian (SAS)

AF:

0.00293

AC:

188

AN:

64182

European-Finnish (FIN)

AF:

0.0814

AC:

3675

AN:

45128

Middle Eastern (MID)

AF:

0.00863

AC:

AN:

3014

European-Non Finnish (NFE)

AF:

0.114

AC:

56756

AN:

498416

Other (OTH)

AF:

0.0808

AC:

2952

AN:

36520

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2967

5935

8902

11870

14837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0726

AC:

11047

AN:

152226

Hom.:

531

Cov.:

AF XY:

0.0677

AC XY:

5034

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0486

AC:

2019

AN:

41542

American (AMR)

AF:

0.0355

AC:

543

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0398

AC:

138

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00124

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0786

AC:

834

AN:

10612

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7321

AN:

67978

Other (OTH)

AF:

0.0549

AC:

116

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

518

1036

1553

2071

2589

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.119

Hom.:

1077

Bravo

AF:

0.0689

Asia WGS

AF:

0.00837

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

-0.12

Splicing

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

Publications

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rs3132449

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