rs3129196

Variant names:

• chr6-33103931-G-A
• rs3129196

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
COL11A2P1		n.33103931G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A2P1	ENST00000441798.1	n.637+7C>T		splice_region_variant, intron_variant	Intron 5 of 5	6

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

African (AFR) AF: 0.451 AC: 6842 AN: 15186

American (AMR) AF: 0.162 AC: 6463 AN: 39854

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 2107 AN: 16218

East Asian (EAS) AF: 0.186 AC: 3606 AN: 19384

South Asian (SAS) AF: 0.253 AC: 17570 AN: 69526

European-Finnish (FIN) AF: 0.229 AC: 9346 AN: 40724

Middle Eastern (MID) AF: 0.228 AC: 807 AN: 3536

European-Non Finnish (NFE) AF: 0.255 AC: 76324 AN: 299096

Other (OTH) AF: 0.256 AC: 6564 AN: 25596

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

African (AFR) AF: 0.411 AC: 17022 AN: 41428

American (AMR) AF: 0.219 AC: 3343 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3470

East Asian (EAS) AF: 0.151 AC: 778 AN: 5162

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4814

European-Finnish (FIN) AF: 0.217 AC: 2294 AN: 10560

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15590 AN: 67954

Other (OTH) AF: 0.267 AC: 562 AN: 2108

Alfa AF: 0.271 Hom.: 913

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs3129196; hg19: chr6-33071708;