rs3128925

Positions:

• chr6-33103823-C-A
• chr6-33103823-C-T

Variant summary

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

The ENST00000441798.1(COL11A2P1):​n.647G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 683,990 control chromosomes in the GnomAD database, including 19,146 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 (6210 hom., cov: 30)
  • Exomes 𝑓: 0.21 (12936 hom.)
• Consequence: COL11A2P1 ENST00000441798.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

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=-0.62).
• 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.647G>T		non_coding_transcript_exon_variant	6/6

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41341 AN: 151750 Hom.: 6203 Cov.: 30

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: 0.218

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.265

GnomAD4 exome AF: 0.209 AC: 111351 AN: 532120 Hom.: 12936 Cov.: 4 AF XY: 0.210 AC XY: 61506 AN XY: 292310

Gnomad4 AFR exome AF: 0.408

Gnomad4 AMR exome AF: 0.157

Gnomad4 ASJ exome AF: 0.117

Gnomad4 EAS exome AF: 0.147

Gnomad4 SAS exome AF: 0.248

Gnomad4 FIN exome AF: 0.210

Gnomad4 NFE exome AF: 0.206

Gnomad4 OTH exome AF: 0.224

GnomAD4 genome AF: 0.272 AC: 41366 AN: 151870 Hom.: 6210 Cov.: 30 AF XY: 0.268 AC XY: 19900 AN XY: 74246

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.265

Alfa AF: 0.175 Hom.: 514

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	-0.62
CADD	Benign	15
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3128925; hg19: chr6-33071600;