rs2064476

Positions:

• chr6-33105545-A-G

Variant summary

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

The ENST00000441798.1(COL11A2P1):​n.577+422T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,942 control chromosomes in the GnomAD database, including 11,339 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 0.37 (11339 hom., cov: 31)
• Consequence: COL11A2P1 ENST00000441798.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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.577+422T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55697 AN: 151824 Hom.: 11316 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.367 AC: 55749 AN: 151942 Hom.: 11339 Cov.: 31 AF XY: 0.362 AC XY: 26918 AN XY: 74316

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.381

Alfa AF: 0.312 Hom.: 10977

Bravo AF: 0.373

Asia WGS AF: 0.500 AC: 1738 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	0.27
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2064476; hg19: chr6-33073322;