rs12538381

Variant names:

• chr7-101498909-C-T
• rs12538381
• NM_001278563.3:c.386-34173C>T

Variant summary

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

The NM_001278563.3(COL26A1):​c.386-34173C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,164 control chromosomes in the GnomAD database, including 860 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 0.10 (860 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 2 publications found

Genes affected

COL26A1 (HGNC:18038): (collagen type XXVI alpha 1 chain) This gene encodes a protein containing an emilin domain and two collagen stretches. This gene may be associated with aspirin-intolerant asthma. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2013]

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 = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278563.3. 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
	COL26A1	NM_001278563.3	MANE Select	c.386-34173C>T		intron	N/A	NP_001265492.1
	COL26A1	NM_133457.5		c.380-34173C>T		intron	N/A	NP_597714.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL26A1	ENST00000313669.12	TSL:1 MANE Select	c.386-34173C>T		intron	N/A	ENSP00000318234.8
	COL26A1	ENST00000613501.1	TSL:1	c.380-34173C>T		intron	N/A	ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15846 AN: 152046 Hom.: 857 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.104 AC: 15880 AN: 152164 Hom.: 860 Cov.: 32 AF XY: 0.105 AC XY: 7823 AN XY: 74392

African (AFR) AF: 0.127 AC: 5254 AN: 41514

American (AMR) AF: 0.0941 AC: 1437 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3470

East Asian (EAS) AF: 0.0939 AC: 484 AN: 5154

South Asian (SAS) AF: 0.100 AC: 484 AN: 4822

European-Finnish (FIN) AF: 0.0905 AC: 959 AN: 10600

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0962 AC: 6544 AN: 68010

Other (OTH) AF: 0.100 AC: 212 AN: 2114

Alfa AF: 0.0970 Hom.: 937

Bravo AF: 0.104

Asia WGS AF: 0.111 AC: 388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.039
DANN	Benign	0.92
PhyloP100		-2.4
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: rs12538381; hg19: chr7-101142190;