6-33104489-C-T

Variant names:

• chr6-33104489-C-T
• rs2064478

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 0.272 in 151,970 control chromosomes in the GnomAD database, including 6,199 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 (6199 hom., cov: 31)
• Consequence: COL11A2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 39 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=-0.85).
• 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.578-492G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41363 AN: 151852 Hom.: 6192 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.272 AC: 41388 AN: 151970 Hom.: 6199 Cov.: 31 AF XY: 0.268 AC XY: 19919 AN XY: 74324

African (AFR) AF: 0.411 AC: 17002 AN: 41388

American (AMR) AF: 0.219 AC: 3352 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3466

East Asian (EAS) AF: 0.150 AC: 775 AN: 5170

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4820

European-Finnish (FIN) AF: 0.217 AC: 2295 AN: 10580

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15590 AN: 67948

Other (OTH) AF: 0.264 AC: 558 AN: 2110

Alfa AF: 0.238 Hom.: 18245

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	-0.85
CADD	Benign	6.1
DANN	Benign	0.66
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs2064478; hg19: chr6-33072266;