NM_001365672.2:c.41+2930C>T

Variant names:

• chr2-164838226-G-A
• rs1858104
• NM_001365672.2:c.41+2930C>T

Variant summary

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

The NM_001365672.2(COBLL1):​c.41+2930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,150 control chromosomes in the GnomAD database, including 1,856 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 0.13 (1856 hom., cov: 32)
• Consequence: COBLL1 NM_001365672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365672.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COBLL1	NM_001365672.2	MANE Select	c.41+2930C>T		intron	N/A	NP_001352601.1	Q53SF7-4
	COBLL1	NM_001278458.2		c.179+2930C>T		intron	N/A	NP_001265387.1	A0A0D9SG04
	COBLL1	NM_001278460.2		c.179+2930C>T		intron	N/A	NP_001265389.1	A0A0X1KG75

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COBLL1	ENST00000652658.2	MANE Select	c.41+2930C>T		intron	N/A	ENSP00000498242.1	Q53SF7-4
	COBLL1	ENST00000409184.8	TSL:1	c.179+2930C>T		intron	N/A	ENSP00000387326.5	A0A0X1KG75
	COBLL1	ENST00000342193.8	TSL:1	c.41+2930C>T		intron	N/A	ENSP00000341360.4	Q53SF7-3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19941 AN: 152032 Hom.: 1850 Cov.: 32

Gnomad AFR AF: 0.0410

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.131 AC: 19951 AN: 152150 Hom.: 1856 Cov.: 32 AF XY: 0.133 AC XY: 9895 AN XY: 74370

African (AFR) AF: 0.0409 AC: 1699 AN: 41532

American (AMR) AF: 0.285 AC: 4349 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.0637 AC: 329 AN: 5166

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4822

European-Finnish (FIN) AF: 0.196 AC: 2075 AN: 10564

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

European-Non Finnish (NFE) AF: 0.158 AC: 10727 AN: 68010

Other (OTH) AF: 0.135 AC: 285 AN: 2106

Alfa AF: 0.148 Hom.: 3209

Bravo AF: 0.137

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.49
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1858104; hg19: chr2-165694736;