rs9864422

Positions:

• chr3-15185745-C-T

Variant summary

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

The NR_027927.1(COL6A4P1):​n.250-7558G>A variant causes a intron, non coding transcript 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 NR_027927.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
COL6A4P1	NR_027927.1	n.250-7558G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL6A4P1	ENST00000446690.2	n.250-7558G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0710

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.184

Alfa AF: 0.150 Hom.: 293

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9864422; hg19: chr3-15227252;