7-101485301-T-C

Position:

• chr7-101485301-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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/exons	MANE	UniProt
COL26A1	NM_001278563.3	c.385+37514T>C		intron_variant		ENST00000313669.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL26A1	ENST00000313669.12	c.385+37514T>C		intron_variant		1	NM_001278563.3	P4
COL26A1	ENST00000613501.1	c.379+37514T>C		intron_variant		1		A1

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

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.602

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

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: rs1543883; hg19: chr7-101128582;