rs10195252

chr2-164656581-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000495084.1(COBLL1):n.182-2667A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COBLL1	ENST00000495084.1	n.182-2667A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.0891

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.416

Alfa AF: 0.407 Hom.: 19677

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10195252; hg19: chr2-165513091;