rs3117234

Variant names:

• chr6-33106207-A-G
• rs3117234

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 0.302 in 179,472 control chromosomes in the GnomAD database, including 9,446 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 0.28 (6471 hom., cov: 32)
  • Exomes 𝑓: 0.43 (2975 hom.)
• Consequence: COL11A2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 21 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A2P1		n.33106207A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A2P1	ENST00000441798.1	n.411-74T>C		intron_variant	Intron 3 of 5	6

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42356 AN: 152066 Hom.: 6464 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.434 AC: 11852 AN: 27288 Hom.: 2975 AF XY: 0.424 AC XY: 6041 AN XY: 14248

African (AFR) AF: 0.666 AC: 880 AN: 1322

American (AMR) AF: 0.408 AC: 350 AN: 858

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 228 AN: 650

East Asian (EAS) AF: 0.264 AC: 639 AN: 2416

South Asian (SAS) AF: 0.352 AC: 476 AN: 1352

European-Finnish (FIN) AF: 0.375 AC: 1351 AN: 3600

Middle Eastern (MID) AF: 0.409 AC: 95 AN: 232

European-Non Finnish (NFE) AF: 0.463 AC: 6954 AN: 15030

Other (OTH) AF: 0.481 AC: 879 AN: 1828

GnomAD4 genome AF: 0.278 AC: 42381 AN: 152184 Hom.: 6471 Cov.: 32 AF XY: 0.274 AC XY: 20369 AN XY: 74410

African (AFR) AF: 0.415 AC: 17224 AN: 41484

American (AMR) AF: 0.225 AC: 3444 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3470

East Asian (EAS) AF: 0.150 AC: 780 AN: 5190

South Asian (SAS) AF: 0.263 AC: 1270 AN: 4828

European-Finnish (FIN) AF: 0.221 AC: 2345 AN: 10598

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16085 AN: 67998

Other (OTH) AF: 0.271 AC: 571 AN: 2110

Alfa AF: 0.257 Hom.: 6403

Bravo AF: 0.280

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.28
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3117234; hg19: chr6-33073984;