rs9864422

Variant names:

• chr3-15185745-C-T
• rs9864422
• ENST00000446690.2:n.250-7558G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446690.2(COL6A4P1):​n.250-7558G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,090 control chromosomes in the GnomAD database, including 2,773 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 0.17 (2773 hom., cov: 32)
• Consequence: COL6A4P1 ENST00000446690.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 8 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL6A4P1	NR_027927.1	n.250-7558G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL6A4P1	ENST00000446690.2	n.250-7558G>A		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26425 AN: 151972 Hom.: 2751 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0710

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.174 AC: 26495 AN: 152090 Hom.: 2773 Cov.: 32 AF XY: 0.179 AC XY: 13290 AN XY: 74358

African (AFR) AF: 0.195 AC: 8101 AN: 41500

American (AMR) AF: 0.200 AC: 3059 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0710 AC: 246 AN: 3466

East Asian (EAS) AF: 0.482 AC: 2492 AN: 5172

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4812

European-Finnish (FIN) AF: 0.0989 AC: 1045 AN: 10568

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9520 AN: 67964

Other (OTH) AF: 0.184 AC: 390 AN: 2116

Alfa AF: 0.152 Hom.: 318

Bravo AF: 0.182

Asia WGS AF: 0.410 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
DANN	Benign	0.77
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9864422; hg19: chr3-15227252;