6-33103545-C-G

Variant names:

• chr6-33103545-C-G
• rs3128923
• ENST00000441798.1:n.*249G>C

Variant summary

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

The ENST00000441798.1(COL11A2P1):​n.*249G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,908 control chromosomes in the GnomAD database, including 8,344 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 0.32 (8344 hom., cov: 30)
• Consequence: COL11A2P1 ENST00000441798.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 15 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 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.*249G>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48061 AN: 151790 Hom.: 8324 Cov.: 30

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.317 AC: 48109 AN: 151908 Hom.: 8344 Cov.: 30 AF XY: 0.313 AC XY: 23264 AN XY: 74218

African (AFR) AF: 0.432 AC: 17893 AN: 41392

American (AMR) AF: 0.254 AC: 3885 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2927 AN: 5162

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4818

European-Finnish (FIN) AF: 0.250 AC: 2634 AN: 10544

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 18024 AN: 67946

Other (OTH) AF: 0.321 AC: 675 AN: 2104

Alfa AF: 0.148 Hom.: 281

Bravo AF: 0.319

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.62
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3128923;

hg19: chr6-33071322;