rs10490694

Variant names:

• chr2-164692059-G-A
• rs10490694
• NM_001365672.2:c.3300+162C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-164692059-G-A
• chr2-164692059-G-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.3300+162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,136 control chromosomes in the GnomAD database, including 1,333 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 (1333 hom., cov: 32)
• Consequence: COBLL1 NM_001365672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 12 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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.3300+162C>T		intron	N/A	NP_001352601.1	Q53SF7-4
	COBLL1	NM_001278458.2		c.3615+162C>T		intron	N/A	NP_001265387.1	A0A0D9SG04
	COBLL1	NM_001278460.2		c.3438+162C>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.3300+162C>T		intron	N/A	ENSP00000498242.1	Q53SF7-4
	COBLL1	ENST00000409184.8	TSL:1	c.3438+162C>T		intron	N/A	ENSP00000387326.5	A0A0X1KG75
	COBLL1	ENST00000342193.8	TSL:1	c.3414+162C>T		intron	N/A	ENSP00000341360.4	Q53SF7-3

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19482 AN: 152018 Hom.: 1333 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.128 AC: 19488 AN: 152136 Hom.: 1333 Cov.: 32 AF XY: 0.127 AC XY: 9469 AN XY: 74378

African (AFR) AF: 0.164 AC: 6823 AN: 41504

American (AMR) AF: 0.115 AC: 1756 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.102 AC: 490 AN: 4822

European-Finnish (FIN) AF: 0.0864 AC: 916 AN: 10596

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8552 AN: 67978

Other (OTH) AF: 0.129 AC: 274 AN: 2116

Alfa AF: 0.124 Hom.: 1764

Bravo AF: 0.131

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.60
PhyloP100		-0.56
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: rs10490694; hg19: chr2-165548569;