NM_001278563.3:c.158+13550T>C

Variant names:

• chr7-101376740-T-C
• rs10237610
• NM_001278563.3:c.158+13550T>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.158+13550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,148 control chromosomes in the GnomAD database, including 47,179 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 0.78 (47179 hom., cov: 33)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.158+13550T>C		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.158+13550T>C		intron_variant	Intron 1 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.158+13550T>C		intron_variant	Intron 1 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119237 AN: 152028 Hom.: 47157 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.784 AC: 119304 AN: 152148 Hom.: 47179 Cov.: 33 AF XY: 0.782 AC XY: 58145 AN XY: 74374

African (AFR) AF: 0.709 AC: 29443 AN: 41508

American (AMR) AF: 0.831 AC: 12704 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2855 AN: 3470

East Asian (EAS) AF: 0.514 AC: 2653 AN: 5162

South Asian (SAS) AF: 0.830 AC: 3997 AN: 4816

European-Finnish (FIN) AF: 0.797 AC: 8439 AN: 10592

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56520 AN: 68004

Other (OTH) AF: 0.778 AC: 1641 AN: 2110

Alfa AF: 0.814 Hom.: 190712

Bravo AF: 0.778

Asia WGS AF: 0.662 AC: 2303 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	0.95
DANN	Benign	0.33
PhyloP100		-0.60
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: rs10237610; hg19: chr7-101020021;