rs10264271

Positions:

• chr7-101527894-G-A

Variant summary

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

The NM_001278563.3(COL26A1):​c.386-5188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,828 control chromosomes in the GnomAD database, including 6,899 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 0.29 (6899 hom., cov: 31)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.386-5188G>A		intron_variant		ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.386-5188G>A		intron_variant		1	NM_001278563.3	ENSP00000318234	P4
COL26A1	ENST00000613501.1	c.380-5188G>A		intron_variant		1		ENSP00000482102	A1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43586 AN: 151710 Hom.: 6883 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0980

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.287 AC: 43633 AN: 151828 Hom.: 6899 Cov.: 31 AF XY: 0.285 AC XY: 21152 AN XY: 74202

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.0981

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.248

Alfa AF: 0.242 Hom.: 8833

Bravo AF: 0.287

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.71

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: rs10264271; hg19: chr7-101171175;