NM_001278563.3:c.386-1264G>A

Variant names:

• chr7-101531818-G-A
• rs17470799
• NM_001278563.3:c.386-1264G>A

Variant summary

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

The NM_001278563.3(COL26A1):​c.386-1264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,672 control chromosomes in the GnomAD database, including 906 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 0.11 (906 hom., cov: 31)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.386-1264G>A		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.386-1264G>A		intron_variant	Intron 3 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.380-1264G>A		intron_variant	Intron 3 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 15992 AN: 151556 Hom.: 906 Cov.: 31

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0645

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.105 AC: 15991 AN: 151672 Hom.: 906 Cov.: 31 AF XY: 0.107 AC XY: 7916 AN XY: 74058

African (AFR) AF: 0.0884 AC: 3653 AN: 41322

American (AMR) AF: 0.138 AC: 2096 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3468

East Asian (EAS) AF: 0.0645 AC: 333 AN: 5164

South Asian (SAS) AF: 0.0802 AC: 384 AN: 4790

European-Finnish (FIN) AF: 0.121 AC: 1268 AN: 10470

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7335 AN: 67916

Other (OTH) AF: 0.104 AC: 217 AN: 2096

Alfa AF: 0.106 Hom.: 1880

Bravo AF: 0.105

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.87
DANN	Benign	0.70
PhyloP100		-0.69
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: rs17470799; hg19: chr7-101175099;