3-130252258-T-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000293535 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504443.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL6A4P2	NR_027898.1		n.1495+949T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL6A4P2	ENST00000504443.6	TSL:6	n.1456+949T>A		intron	N/A
	ENSG00000293535	ENST00000507516.5	TSL:5	n.1989+949T>A		intron	N/A

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

African (AFR) AF: 0.372 AC: 15421 AN: 41498

American (AMR) AF: 0.209 AC: 3200 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3472

East Asian (EAS) AF: 0.191 AC: 988 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1215 AN: 4832

European-Finnish (FIN) AF: 0.184 AC: 1953 AN: 10598

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13193 AN: 67982

Other (OTH) AF: 0.236 AC: 499 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.33
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs9813712; hg19: chr3-129971101;