7-101434774-G-C

Variant names:

• chr7-101434774-G-C
• rs13238748
• NM_001278563.3:c.282-12910G>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.282-12910G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,004 control chromosomes in the GnomAD database, including 18,053 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 0.48 (18053 hom., cov: 31)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.916
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.282-12910G>C		intron_variant	Intron 2 of 12	ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.282-12910G>C		intron_variant	Intron 2 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.282-12916G>C		intron_variant	Intron 2 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72290 AN: 151886 Hom.: 18050 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.476 AC: 72324 AN: 152004 Hom.: 18053 Cov.: 31 AF XY: 0.476 AC XY: 35350 AN XY: 74294

African (AFR) AF: 0.325 AC: 13478 AN: 41466

American (AMR) AF: 0.582 AC: 8881 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1743 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2470 AN: 5152

South Asian (SAS) AF: 0.533 AC: 2566 AN: 4810

European-Finnish (FIN) AF: 0.495 AC: 5232 AN: 10562

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36089 AN: 67972

Other (OTH) AF: 0.498 AC: 1052 AN: 2112

Alfa AF: 0.328 Hom.: 747

Bravo AF: 0.475

Asia WGS AF: 0.496 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		0.92
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: rs13238748; hg19: chr7-101078055;