rs1008064

Variant names:

• chr7-101472937-T-C
• rs1008064
• NM_001278563.3:c.385+25150T>C

Variant summary

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

The NM_001278563.3(COL26A1):​c.385+25150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,034 control chromosomes in the GnomAD database, including 33,487 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 0.64 (33487 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278563.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL26A1	NM_001278563.3	MANE Select	c.385+25150T>C		intron	N/A	NP_001265492.1	Q96A83-1
	COL26A1	NM_133457.5		c.379+25150T>C		intron	N/A	NP_597714.2	Q96A83-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL26A1	ENST00000313669.12	TSL:1 MANE Select	c.385+25150T>C		intron	N/A	ENSP00000318234.8	Q96A83-1
	COL26A1	ENST00000613501.1	TSL:1	c.379+25150T>C		intron	N/A	ENSP00000482102.1	Q96A83-2
	COL26A1	ENST00000913313.1		c.385+25150T>C		intron	N/A	ENSP00000583372.1

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97259 AN: 151916 Hom.: 33428 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.641 AC: 97384 AN: 152034 Hom.: 33487 Cov.: 32 AF XY: 0.638 AC XY: 47373 AN XY: 74286

African (AFR) AF: 0.906 AC: 37621 AN: 41514

American (AMR) AF: 0.538 AC: 8204 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2505 AN: 5144

South Asian (SAS) AF: 0.621 AC: 2987 AN: 4808

European-Finnish (FIN) AF: 0.515 AC: 5439 AN: 10554

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36993 AN: 67974

Other (OTH) AF: 0.615 AC: 1298 AN: 2110

Alfa AF: 0.569 Hom.: 41856

Bravo AF: 0.648

Asia WGS AF: 0.581 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.50
PhyloP100		-1.9
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: rs1008064; hg19: chr7-101116218;