rs9640666

chr7-101388988-G-Achr7-101388988-G-T

Variant summary

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

The NM_001278563.3(COL26A1):c.158+25798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 289,214 control chromosomes in the GnomAD database, including 32,914 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 0.44 (15694 hom., cov: 32)
  • Exomes 𝑓: 0.50 (17220 hom.)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL26A1	NM_001278563.3	c.158+25798G>A		intron_variant		ENST00000313669.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL26A1	ENST00000313669.12	c.158+25798G>A		intron_variant		1	NM_001278563.3	P4
COL26A1	ENST00000613501.1	c.158+25798G>A		intron_variant		1		A1
	ENST00000413033.1	n.93C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66439 AN: 151920 Hom.: 15693 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.441

GnomAD4 exome AF: 0.496 AC: 67996 AN: 137176 Hom.: 17220 Cov.: 0 AF XY: 0.499 AC XY: 42480 AN XY: 85186

Gnomad4 AFR exome AF: 0.238

Gnomad4 AMR exome AF: 0.614

Gnomad4 ASJ exome AF: 0.470

Gnomad4 EAS exome AF: 0.402

Gnomad4 SAS exome AF: 0.547

Gnomad4 FIN exome AF: 0.492

Gnomad4 NFE exome AF: 0.486

Gnomad4 OTH exome AF: 0.471

GnomAD4 genome AF: 0.437 AC: 66447 AN: 152038 Hom.: 15694 Cov.: 32 AF XY: 0.442 AC XY: 32855 AN XY: 74298

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.438

Alfa AF: 0.493 Hom.: 16857

Bravo AF: 0.429

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.41
Dann	Benign	0.64

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: rs9640666; hg19: chr7-101032269;