rs7639618

Variant names:

• chr3-15174922-C-T
• rs7639618
• ENST00000446690.2:n.1282G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.95
• Publications: 37 publications found

Genes affected

COL6A4P1 (HGNC:):

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446690.2. 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
	COL6A4P1	NR_027927.1		n.1282G>A		non_coding_transcript_exon	Exon 3 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL6A4P1	ENST00000446690.2	TSL:2	n.1282G>A		non_coding_transcript_exon	Exon 3 of 5
	COL6A4P1	ENST00000487147.5	TSL:6	n.1106G>A		non_coding_transcript_exon	Exon 3 of 13
	COL6A4P1	ENST00000491915.1	TSL:5	n.182G>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28044 AN: 152016 Hom.: 2983 Cov.: 32

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

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.: 0 AF XY: 0.209 AC XY: 36524 AN XY: 174526

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

GnomAD4 genome AF: 0.185 AC: 28115 AN: 152134 Hom.: 3004 Cov.: 32 AF XY: 0.189 AC XY: 14070 AN XY: 74392

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: 37 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10831 AN: 67994

Other (OTH) AF: 0.191 AC: 404 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		3.0

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: rs7639618;

hg19: chr3-15216429;