NM_001278563.3:c.158+4683G>A

Variant names:

• chr7-101367873-G-A
• rs4729697
• NM_001278563.3:c.158+4683G>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.158+4683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,836 control chromosomes in the GnomAD database, including 27,112 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 0.58 (27112 hom., cov: 31)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 5 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.158+4683G>A		intron_variant	Intron 1 of 12	ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.158+4683G>A		intron_variant	Intron 1 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.158+4683G>A		intron_variant	Intron 1 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87939 AN: 151718 Hom.: 27049 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.580 AC: 88062 AN: 151836 Hom.: 27112 Cov.: 31 AF XY: 0.576 AC XY: 42762 AN XY: 74176

African (AFR) AF: 0.799 AC: 33096 AN: 41430

American (AMR) AF: 0.446 AC: 6803 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1863 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3445 AN: 5146

South Asian (SAS) AF: 0.493 AC: 2367 AN: 4802

European-Finnish (FIN) AF: 0.468 AC: 4934 AN: 10532

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33889 AN: 67910

Other (OTH) AF: 0.576 AC: 1212 AN: 2104

Alfa AF: 0.573 Hom.: 4053

Bravo AF: 0.590

Asia WGS AF: 0.585 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.32
PhyloP100		-1.1
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: rs4729697; hg19: chr7-101011154;