2-164683151-T-C

Position:

• chr2-164683151-T-C

Variant summary

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

The NM_001365672.2(COBLL1):​c.*2795A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,596 control chromosomes in the GnomAD database, including 18,600 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 (18599 hom., cov: 30)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: COBLL1 NM_001365672.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

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]

COBLL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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/exons	MANE	Protein	UniProt
COBLL1	NM_001365672.2	c.*2795A>G		3_prime_UTR_variant	14/14	ENST00000652658.2	NP_001352601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COBLL1	ENST00000652658	c.*2795A>G		3_prime_UTR_variant	14/14		NM_001365672.2	ENSP00000498242.1
COBLL1	ENST00000375458	c.*2795A>G		3_prime_UTR_variant	13/13	1		ENSP00000364607.2
COBLL1	ENST00000495084.1	n.126+9070A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70077 AN: 151468 Hom.: 18548 Cov.: 30

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.418

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.463 AC: 70171 AN: 151588 Hom.: 18599 Cov.: 30 AF XY: 0.453 AC XY: 33583 AN XY: 74108

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0902

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.415

Alfa AF: 0.380 Hom.: 3561

Bravo AF: 0.474

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
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: rs6717858; hg19: chr2-165539661;