rs3130210

chr6-33104952-G-T

Variant summary

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

The ENST00000441798.1(COL11A2P1):n.578-955C>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 0.272 in 152,070 control chromosomes in the GnomAD database, including 6,207 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 0.27 (6207 hom., cov: 32)
• Consequence: COL11A2P1 ENST00000441798.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

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 (AFR) allele frequency at 95% confidence interval = 0.405 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.578-955C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41378 AN: 151952 Hom.: 6200 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.272 AC: 41403 AN: 152070 Hom.: 6207 Cov.: 32 AF XY: 0.268 AC XY: 19911 AN XY: 74346

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.266

Alfa AF: 0.255 Hom.: 1141

Bravo AF: 0.274

Asia WGS AF: 0.267 AC: 928 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	3.6
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130210; hg19: chr6-33072729;