chr7-101485301-T-C

Variant names:

• chr7-101485301-T-C
• rs1543883
• NM_001278563.3:c.385+37514T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278563.3(COL26A1):​c.385+37514T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,108 control chromosomes in the GnomAD database, including 32,455 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 0.63 (32455 hom., cov: 33)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.385+37514T>C		intron_variant	Intron 3 of 12	ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.385+37514T>C		intron_variant	Intron 3 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.379+37514T>C		intron_variant	Intron 3 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95409 AN: 151988 Hom.: 32392 Cov.: 33

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.628 AC: 95537 AN: 152108 Hom.: 32455 Cov.: 33 AF XY: 0.625 AC XY: 46514 AN XY: 74366

African (AFR) AF: 0.905 AC: 37610 AN: 41564

American (AMR) AF: 0.526 AC: 8033 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2545 AN: 5172

South Asian (SAS) AF: 0.614 AC: 2961 AN: 4822

European-Finnish (FIN) AF: 0.506 AC: 5345 AN: 10570

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35429 AN: 67918

Other (OTH) AF: 0.602 AC: 1273 AN: 2114

Alfa AF: 0.605 Hom.: 2796

Bravo AF: 0.635

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.21
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: rs1543883; hg19: chr7-101128582;