NM_001278563.3:c.159-199G>A

Variant names:

• chr7-101419778-G-A
• rs10254310
• NM_001278563.3:c.159-199G>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.159-199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,062 control chromosomes in the GnomAD database, including 47,642 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 0.79 (47642 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• 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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.159-199G>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.159-199G>A		intron_variant	Intron 1 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.159-199G>A		intron_variant	Intron 1 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119401 AN: 151944 Hom.: 47611 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.786 AC: 119487 AN: 152062 Hom.: 47642 Cov.: 32 AF XY: 0.782 AC XY: 58085 AN XY: 74324

African (AFR) AF: 0.676 AC: 28043 AN: 41468

American (AMR) AF: 0.836 AC: 12764 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3120 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2652 AN: 5120

South Asian (SAS) AF: 0.800 AC: 3848 AN: 4812

European-Finnish (FIN) AF: 0.780 AC: 8268 AN: 10602

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57937 AN: 67996

Other (OTH) AF: 0.814 AC: 1722 AN: 2116

Alfa AF: 0.833 Hom.: 222696

Bravo AF: 0.783

Asia WGS AF: 0.649 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.8
DANN	Benign	0.86
PhyloP100		-0.26
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: rs10254310; hg19: chr7-101063059;