7-101522092-A-G

Variant names:

• chr7-101522092-A-G
• rs1859634
• NM_001278563.3:c.386-10990A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278563.3(COL26A1):​c.386-10990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,976 control chromosomes in the GnomAD database, including 37,434 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 0.68 (37434 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.386-10990A>G		intron_variant	Intron 3 of 12	ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.386-10990A>G		intron_variant	Intron 3 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.380-10990A>G		intron_variant	Intron 3 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102934 AN: 151858 Hom.: 37380 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.678 AC: 103032 AN: 151976 Hom.: 37434 Cov.: 32 AF XY: 0.669 AC XY: 49704 AN XY: 74278

African (AFR) AF: 0.924 AC: 38332 AN: 41504

American (AMR) AF: 0.596 AC: 9099 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2295 AN: 3468

East Asian (EAS) AF: 0.153 AC: 790 AN: 5160

South Asian (SAS) AF: 0.499 AC: 2402 AN: 4818

European-Finnish (FIN) AF: 0.574 AC: 6040 AN: 10514

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41920 AN: 67930

Other (OTH) AF: 0.667 AC: 1410 AN: 2114

Alfa AF: 0.679 Hom.: 4971

Bravo AF: 0.685

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.36
PhyloP100		-1.2
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: rs1859634; hg19: chr7-101165373;