rs10195252

Variant names:

• chr2-164656581-T-C
• rs10195252
• ENST00000495084.1:n.182-2667A>G

Variant summary

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

The ENST00000495084.1(COBLL1):​n.182-2667A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,004 control chromosomes in the GnomAD database, including 18,814 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 (18814 hom., cov: 32)
• Consequence: COBLL1 ENST00000495084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 179 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COBLL1	ENST00000495084.1	n.182-2667A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70528 AN: 151886 Hom.: 18766 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0889

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.465 AC: 70619 AN: 152004 Hom.: 18814 Cov.: 32 AF XY: 0.454 AC XY: 33703 AN XY: 74310

African (AFR) AF: 0.730 AC: 30277 AN: 41454

American (AMR) AF: 0.316 AC: 4833 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3470

East Asian (EAS) AF: 0.0891 AC: 460 AN: 5160

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4828

European-Finnish (FIN) AF: 0.330 AC: 3487 AN: 10552

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

European-Non Finnish (NFE) AF: 0.409 AC: 27786 AN: 67958

Other (OTH) AF: 0.416 AC: 875 AN: 2104

Alfa AF: 0.420 Hom.: 51472

Bravo AF: 0.477

Asia WGS AF: 0.223 AC: 777 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	2.7
DANN	Benign	0.56
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10195252; hg19: chr2-165513091;