7-101486484-G-T

Position:

• chr7-101486484-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.385+38697G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 152,270 control chromosomes in the GnomAD database, including 1,352 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 0.093 (1352 hom., cov: 33)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.385+38697G>T		intron_variant		ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.385+38697G>T		intron_variant		1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.379+38697G>T		intron_variant		1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14170 AN: 152152 Hom.: 1340 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0934 AC: 14222 AN: 152270 Hom.: 1352 Cov.: 33 AF XY: 0.0924 AC XY: 6883 AN XY: 74462

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.0385

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0298

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0727

Gnomad4 NFE AF: 0.0319

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0274 Hom.: 38

Bravo AF: 0.0970

Asia WGS AF: 0.0390 AC: 136 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	0.0040
DANN	Benign	0.52

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: rs73712171; hg19: chr7-101129765;