6-33104463-C-T

Variant names:

• chr6-33104463-C-T
• rs2064479

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 0.312 in 151,984 control chromosomes in the GnomAD database, including 8,138 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 0.31 (8138 hom., cov: 31)
• Consequence: COL11A2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 19 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A2P1		n.33104463C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A2P1	ENST00000441798.1	n.578-466G>A		intron_variant	Intron 4 of 5	6

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47292 AN: 151864 Hom.: 8115 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.312 AC: 47344 AN: 151984 Hom.: 8138 Cov.: 31 AF XY: 0.309 AC XY: 22939 AN XY: 74304

African (AFR) AF: 0.430 AC: 17801 AN: 41404

American (AMR) AF: 0.249 AC: 3808 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2937 AN: 5162

South Asian (SAS) AF: 0.281 AC: 1359 AN: 4828

European-Finnish (FIN) AF: 0.245 AC: 2592 AN: 10562

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17543 AN: 67958

Other (OTH) AF: 0.316 AC: 665 AN: 2106

Alfa AF: 0.272 Hom.: 5833

Bravo AF: 0.314

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.23
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2064479; hg19: chr6-33072240;