dbSNP rs7639618: COL6A4P1:n.1282G>A (chr3-15174922-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000446690.2(COL6A4P1):n.1282G>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 0.195 in 458,898 control chromosomes in the GnomAD database, including 10,351 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 0.18 ( 3004 hom., cov: 32)

Exomes 𝑓: 0.20 ( 7347 hom. )

Consequence

COL6A4P1
ENST00000446690.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.95

Publications

37 publications found

Variant links:

Genes affected

COL6A4P1 (HGNC:):

COL6A4P1 links:

COL6A4P1 (HGNC:33484): (collagen type VI alpha 4 pseudogene 1) This transcribed pseudogene represents the 5' end of a presumed ortholog to a mouse gene which encodes a collagen VI alpha 4 chain protein (GeneID 68553). No complete ORF of comparable size to the mouse protein is found in this gene. The predicted protein lacks a signal peptide; however, this truncated collagen polypeptide may have achieved a different function as suggested by PubMed ID: 18622395. Evidence of in vivo translation is incomplete. A large chromosome break separates this pseudogene from the 3' end of the presumed ortholog (COL6A4P2, GeneID 646300) which is located downstream at chromosome 3q21.3. [provided by RefSeq, Jun 2009]

COL6A4P1 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.21).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL6A4P1	NR_027927.1 link	n.1282G>A		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
COL6A4P1	ENST00000446690.2 link	n.1282G>A	non_coding_transcript_exon_variant	Exon 3 of 5	2
COL6A4P1	ENST00000487147.5 link	n.1106G>A	non_coding_transcript_exon_variant	Exon 3 of 13	6
COL6A4P1	ENST00000491915.1 link	n.182G>A	non_coding_transcript_exon_variant	Exon 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

28044

AN:

152016

Hom.:

2983

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.0835

Gnomad EAS

AF:

0.493

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.183

GnomAD2 exomes

AF:

0.217

AC:

29299

AN:

134806

AF XY:

0.220

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.231

Gnomad ASJ exome

AF:

0.0773

Gnomad EAS exome

AF:

0.497

Gnomad FIN exome

AF:

0.138

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.176

GnomAD4 exome

AF:

0.200

AC:

61438

AN:

306764

Hom.:

7347

Cov.:

AF XY:

0.209

AC XY:

36524

AN XY:

174526

show subpopulations

African (AFR)

AF:

0.186

AC:

1614

AN:

8676

American (AMR)

AF:

0.230

AC:

6255

AN:

27204

Ashkenazi Jewish (ASJ)

AF:

0.0783

AC:

841

AN:

10734

East Asian (EAS)

AF:

0.482

AC:

4644

AN:

9636

South Asian (SAS)

AF:

0.295

AC:

17513

AN:

59274

European-Finnish (FIN)

AF:

0.140

AC:

1868

AN:

13374

Middle Eastern (MID)

AF:

0.126

AC:

354

AN:

2804

European-Non Finnish (NFE)

AF:

0.159

AC:

25609

AN:

160688

Other (OTH)

AF:

0.191

AC:

2740

AN:

14374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

2760

5519

8279

11038

13798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.185

AC:

28115

AN:

152134

Hom.:

3004

Cov.:

AF XY:

0.189

AC XY:

14070

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.188

AC:

7819

AN:

41484

American (AMR)

AF:

0.204

AC:

3125

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0835

AC:

290

AN:

3472

East Asian (EAS)

AF:

0.493

AC:

2543

AN:

5162

South Asian (SAS)

AF:

0.321

AC:

1545

AN:

4818

European-Finnish (FIN)

AF:

0.129

AC:

1367

AN:

10604

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10831

AN:

67994

Other (OTH)

AF:

0.191

AC:

404

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1116

2232

3348

4464

5580

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.169

Hom.:

10286

Bravo

AF:

0.189

Asia WGS

AF:

0.413

AC:

1436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.21

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

3.0

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