rs17135512

Variant names:

• chr7-101499248-A-G
• rs17135512
• NM_001278563.3:c.386-33834A>G

Variant summary

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

The NM_001278563.3(COL26A1):​c.386-33834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0924 in 152,192 control chromosomes in the GnomAD database, including 669 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 0.092 (669 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.0941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.386-33834A>G		intron_variant	Intron 3 of 12	ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.386-33834A>G		intron_variant	Intron 3 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.380-33834A>G		intron_variant	Intron 3 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 14044 AN: 152074 Hom.: 668 Cov.: 32

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0944

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0961

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.0924 AC: 14070 AN: 152192 Hom.: 669 Cov.: 32 AF XY: 0.0931 AC XY: 6926 AN XY: 74400

African (AFR) AF: 0.0847 AC: 3520 AN: 41534

American (AMR) AF: 0.0906 AC: 1384 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3472

East Asian (EAS) AF: 0.0938 AC: 484 AN: 5158

South Asian (SAS) AF: 0.100 AC: 484 AN: 4824

European-Finnish (FIN) AF: 0.0908 AC: 962 AN: 10600

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

European-Non Finnish (NFE) AF: 0.0961 AC: 6533 AN: 68002

Other (OTH) AF: 0.0932 AC: 197 AN: 2114

Alfa AF: 0.0938 Hom.: 1049

Bravo AF: 0.0906

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.73
PhyloP100		0.38
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: rs17135512; hg19: chr7-101142529;