rs4282438

Variant names:

• chr6-33104395-T-G
• rs4282438

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 0.0355 in 152,358 control chromosomes in the GnomAD database, including 546 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 0.036 (546 hom., cov: 32)
• Consequence: COL11A2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 36 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A2P1		n.33104395T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A2P1	ENST00000441798.1	n.578-398A>C		intron_variant	Intron 4 of 5	6

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5391 AN: 152240 Hom.: 535 Cov.: 32

Gnomad AFR AF: 0.00825

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0355 AC: 5414 AN: 152358 Hom.: 546 Cov.: 32 AF XY: 0.0368 AC XY: 2745 AN XY: 74510

African (AFR) AF: 0.00830 AC: 345 AN: 41586

American (AMR) AF: 0.0283 AC: 433 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2157 AN: 5184

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4832

European-Finnish (FIN) AF: 0.0280 AC: 298 AN: 10624

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0285 AC: 1936 AN: 68034

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0379 Hom.: 792

Bravo AF: 0.0358

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs4282438; hg19: chr6-33072172;