ENST00000504443.6:n.1456+949T>A

Variant names:

• chr3-130252258-T-A
• rs9813712
• ENST00000504443.6:n.1456+949T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504443.6(COL6A4P2):​n.1456+949T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,166 control chromosomes in the GnomAD database, including 5,177 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 0.25 (5177 hom., cov: 32)
• Consequence: COL6A4P2 ENST00000504443.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

COL6A4P2 (HGNC:38501): (collagen type VI alpha 4 pseudogene 2) This transcribed pseudogene represents the 3' end of a presumed ortholog to a mouse gene which encodes a collagen VI alpha 4 chain protein (GeneID 68553). The predicted ORF contains multiple premature stop codons. A large chromosome break separates this pseudogene from the 5' end of the presumed ortholog (DVWA, GeneID 344875) which is located upstream at chromosome 3p24.3. [provided by RefSeq, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL6A4P2	NR_027898.1	n.1495+949T>A		intron_variant	Intron 19 of 22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL6A4P2	ENST00000504443.6	n.1456+949T>A		intron_variant	Intron 20 of 24	6

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37577 AN: 152048 Hom.: 5171 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.236

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.247 AC: 37611 AN: 152166 Hom.: 5177 Cov.: 32 AF XY: 0.243 AC XY: 18049 AN XY: 74402

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.236

Alfa AF: 0.226 Hom.: 534

Bravo AF: 0.259

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9813712; hg19: chr3-129971101;