chr6-33103931-G-A

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 ENST00000441798.1(COL11A2P1):​n.637+7C>T variant causes a splice region, intron 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
• 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441798.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL11A2P1	ENST00000441798.1	TSL:6	n.637+7C>T		splice_region intron	N/A

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 v4.9

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;