7-101438517-G-A

Variant names:

• chr7-101438517-G-A
• rs4727494
• NM_001278563.3:c.282-9167G>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.282-9167G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,130 control chromosomes in the GnomAD database, including 31,532 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 0.60 (31532 hom., cov: 30)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 11 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.282-9167G>A		intron_variant	Intron 2 of 12	ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.282-9167G>A		intron_variant	Intron 2 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.282-9173G>A		intron_variant	Intron 2 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91236 AN: 151012 Hom.: 31532 Cov.: 30

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.604 AC: 91259 AN: 151130 Hom.: 31532 Cov.: 30 AF XY: 0.602 AC XY: 44489 AN XY: 73844

African (AFR) AF: 0.296 AC: 12226 AN: 41348

American (AMR) AF: 0.727 AC: 11000 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2701 AN: 3462

East Asian (EAS) AF: 0.377 AC: 1940 AN: 5142

South Asian (SAS) AF: 0.710 AC: 3415 AN: 4812

European-Finnish (FIN) AF: 0.671 AC: 7051 AN: 10510

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50504 AN: 67458

Other (OTH) AF: 0.659 AC: 1374 AN: 2086

Alfa AF: 0.701 Hom.: 120097

Bravo AF: 0.593

Asia WGS AF: 0.544 AC: 1894 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.35
PhyloP100		-0.22
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: rs4727494; hg19: chr7-101081798;