rs2064479

chr6-33104463-C-T

Variant summary

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

The ENST00000441798.1(COL11A2P1):n.578-466G>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 0.312 in 151,984 control chromosomes in the GnomAD database, including 8,138 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 0.31 (8138 hom., cov: 31)
• Consequence: COL11A2P1 ENST00000441798.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

Genes affected

COL11A2P1 (HGNC:13947): (collagen type XI alpha 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL11A2P1	ENST00000441798.1	n.578-466G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47292 AN: 151864 Hom.: 8115 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.312 AC: 47344 AN: 151984 Hom.: 8138 Cov.: 31 AF XY: 0.309 AC XY: 22939 AN XY: 74304

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.316

Alfa AF: 0.266 Hom.: 3821

Bravo AF: 0.314

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.78
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2064479; hg19: chr6-33072240;