rs3128925

Variant names:

• chr6-33103823-C-A
• rs3128925
• ENST00000441798.1:n.647G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-33103823-C-A
• chr6-33103823-C-T

Variant summary

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

The ENST00000441798.1(COL11A2P1):​n.647G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 683,990 control chromosomes in the GnomAD database, including 19,146 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 (6210 hom., cov: 30)
  • Exomes 𝑓: 0.21 (12936 hom.)
• Consequence: COL11A2P1 ENST00000441798.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 4 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=-0.62).
• 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL11A2P1	ENST00000441798.1	TSL:6	n.647G>T		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41341 AN: 151750 Hom.: 6203 Cov.: 30

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: 0.218

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.265

GnomAD4 exome AF: 0.209 AC: 111351 AN: 532120 Hom.: 12936 Cov.: 4 AF XY: 0.210 AC XY: 61506 AN XY: 292310

African (AFR) AF: 0.408 AC: 5864 AN: 14368

American (AMR) AF: 0.157 AC: 6279 AN: 40030

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 1981 AN: 16978

East Asian (EAS) AF: 0.147 AC: 2878 AN: 19526

South Asian (SAS) AF: 0.248 AC: 17160 AN: 69234

European-Finnish (FIN) AF: 0.210 AC: 8804 AN: 41902

Middle Eastern (MID) AF: 0.214 AC: 721 AN: 3362

European-Non Finnish (NFE) AF: 0.206 AC: 61852 AN: 300794

Other (OTH) AF: 0.224 AC: 5812 AN: 25926

GnomAD4 genome AF: 0.272 AC: 41366 AN: 151870 Hom.: 6210 Cov.: 30 AF XY: 0.268 AC XY: 19900 AN XY: 74246

African (AFR) AF: 0.411 AC: 16989 AN: 41364

American (AMR) AF: 0.219 AC: 3348 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3472

East Asian (EAS) AF: 0.150 AC: 775 AN: 5166

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4810

European-Finnish (FIN) AF: 0.218 AC: 2300 AN: 10558

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15579 AN: 67906

Other (OTH) AF: 0.265 AC: 559 AN: 2110

Alfa AF: 0.183 Hom.: 579

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	-0.62
CADD	Benign	15
DANN	Benign	0.32
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs3128925; hg19: chr6-33071600;