rs13245946

Positions:

• chr7-101531684-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278563.3(COL26A1):​c.386-1398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,124 control chromosomes in the GnomAD database, including 1,126 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 0.12 (1126 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL26A1	NM_001278563.3	c.386-1398C>T		intron_variant		ENST00000313669.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL26A1	ENST00000313669.12	c.386-1398C>T		intron_variant		1	NM_001278563.3	P4
COL26A1	ENST00000613501.1	c.380-1398C>T		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17781 AN: 152006 Hom.: 1128 Cov.: 32

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0695

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.117 AC: 17771 AN: 152124 Hom.: 1126 Cov.: 32 AF XY: 0.117 AC XY: 8683 AN XY: 74366

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0695

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.120

Alfa AF: 0.135 Hom.: 1879

Bravo AF: 0.114

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs13245946; hg19: chr7-101174965;