chr7-101398477-C-A

Position:

• chr7-101398477-C-A

Variant summary

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

The NM_001278563.3(COL26A1):​c.159-21500C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,954 control chromosomes in the GnomAD database, including 32,555 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 0.65 (32555 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.159-21500C>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.159-21500C>A		intron_variant		1	NM_001278563.3	ENSP00000318234	P4
COL26A1	ENST00000613501.1	c.159-21500C>A		intron_variant		1		ENSP00000482102	A1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99187 AN: 151836 Hom.: 32540 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.653 AC: 99243 AN: 151954 Hom.: 32555 Cov.: 32 AF XY: 0.651 AC XY: 48319 AN XY: 74242

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.642

Alfa AF: 0.668 Hom.: 18339

Bravo AF: 0.654

Asia WGS AF: 0.583 AC: 2028 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.63

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: rs6947185; hg19: chr7-101041758;