rs3129196

chr6-33103931-G-A

Variant summary

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

The ENST00000441798.1(COL11A2P1):n.637+7C>T variant causes a splice region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 681,092 control chromosomes in the GnomAD database, including 24,296 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 (6218 hom., cov: 31)
  • Exomes 𝑓: 0.24 (18078 hom.)
• Consequence: COL11A2P1 ENST00000441798.1 splice_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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.637+7C>T		splice_region_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41380 AN: 151854 Hom.: 6211 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.267

GnomAD4 exome AF: 0.245 AC: 129629 AN: 529120 Hom.: 18078 Cov.: 4 AF XY: 0.243 AC XY: 70551 AN XY: 290760

Gnomad4 AFR exome AF: 0.451

Gnomad4 AMR exome AF: 0.162

Gnomad4 ASJ exome AF: 0.130

Gnomad4 EAS exome AF: 0.186

Gnomad4 SAS exome AF: 0.253

Gnomad4 FIN exome AF: 0.229

Gnomad4 NFE exome AF: 0.255

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.272 AC: 41405 AN: 151972 Hom.: 6218 Cov.: 31 AF XY: 0.268 AC XY: 19918 AN XY: 74286

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.219

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: 0.267

Alfa AF: 0.266 Hom.: 848

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	-1.0
Cadd	Benign	0.36
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129196; hg19: chr6-33071708;