rs13389219

Variant names:

• chr2-164672366-C-T
• rs13389219
• NM_001365671.1:c.3478-6465G>A

Variant summary

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

The NM_001365671.1(COBLL1):​c.3478-6465G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,052 control chromosomes in the GnomAD database, including 18,339 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 0.46 (18339 hom., cov: 32)
• Consequence: COBLL1 NM_001365671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.934
• Publications: 117 publications found

Genes affected

COBLL1 (HGNC:23571): (cordon-bleu WH2 repeat protein like 1) Enables cadherin binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COBLL1	NM_001365671.1	c.3478-6465G>A		intron_variant	Intron 14 of 15		NP_001352600.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COBLL1	ENST00000495084.1	n.127-6465G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69399 AN: 151934 Hom.: 18289 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0883

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.457 AC: 69491 AN: 152052 Hom.: 18339 Cov.: 32 AF XY: 0.446 AC XY: 33164 AN XY: 74314

African (AFR) AF: 0.729 AC: 30219 AN: 41474

American (AMR) AF: 0.308 AC: 4708 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3472

East Asian (EAS) AF: 0.0885 AC: 457 AN: 5164

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4824

European-Finnish (FIN) AF: 0.318 AC: 3357 AN: 10556

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26974 AN: 67984

Other (OTH) AF: 0.409 AC: 863 AN: 2110

Alfa AF: 0.410 Hom.: 38712

Bravo AF: 0.470

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.5
DANN	Benign	0.64
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs13389219; hg19: chr2-165528876;