NM_001365672.2:c.41+48489C>T

Variant names:

• chr2-164792667-G-A
• rs10490693
• NM_001365672.2:c.41+48489C>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+48489C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,070 control chromosomes in the GnomAD database, including 1,413 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 0.12 (1413 hom., cov: 32)
• Consequence: COBLL1 NM_001365672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.175 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COBLL1	NM_001365672.2	MANE Select	c.41+48489C>T		intron	N/A	NP_001352601.1
	COBLL1	NM_001278458.2		c.200+7867C>T		intron	N/A	NP_001265387.1
	COBLL1	NM_001278460.2		c.179+48489C>T		intron	N/A	NP_001265389.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COBLL1	ENST00000652658.2	MANE Select	c.41+48489C>T		intron	N/A	ENSP00000498242.1
	COBLL1	ENST00000409184.8	TSL:1	c.179+48489C>T		intron	N/A	ENSP00000387326.5
	COBLL1	ENST00000342193.8	TSL:1	c.41+48489C>T		intron	N/A	ENSP00000341360.4

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17914 AN: 151952 Hom.: 1413 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.0606

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.118 AC: 17913 AN: 152070 Hom.: 1413 Cov.: 32 AF XY: 0.118 AC XY: 8771 AN XY: 74326

African (AFR) AF: 0.0331 AC: 1374 AN: 41484

American (AMR) AF: 0.181 AC: 2764 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3468

East Asian (EAS) AF: 0.0605 AC: 313 AN: 5172

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4812

European-Finnish (FIN) AF: 0.197 AC: 2075 AN: 10552

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.157 AC: 10664 AN: 67988

Other (OTH) AF: 0.118 AC: 249 AN: 2112

Alfa AF: 0.139 Hom.: 3896

Bravo AF: 0.114

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.13
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: rs10490693; hg19: chr2-165649177;