7-101388988-G-A

Variant names:

• chr7-101388988-G-A
• rs9640666
• NM_001278563.3:c.158+25798G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ENSG00000233683 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.158+25798G>A		intron	N/A	NP_001265492.1	Q96A83-1
	COL26A1	NM_133457.5		c.158+25798G>A		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.158+25798G>A		intron	N/A	ENSP00000318234.8	Q96A83-1
	COL26A1	ENST00000613501.1	TSL:1	c.158+25798G>A		intron	N/A	ENSP00000482102.1	Q96A83-2
	COL26A1	ENST00000913313.1		c.158+25798G>A		intron	N/A	ENSP00000583372.1

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

African (AFR) AF: 0.238 AC: 692 AN: 2902

American (AMR) AF: 0.614 AC: 6275 AN: 10218

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1328 AN: 2824

East Asian (EAS) AF: 0.402 AC: 2089 AN: 5192

South Asian (SAS) AF: 0.547 AC: 11261 AN: 20598

European-Finnish (FIN) AF: 0.492 AC: 3725 AN: 7566

Middle Eastern (MID) AF: 0.470 AC: 190 AN: 404

European-Non Finnish (NFE) AF: 0.486 AC: 39544 AN: 81328

Other (OTH) AF: 0.471 AC: 2892 AN: 6144

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

African (AFR) AF: 0.250 AC: 10377 AN: 41480

American (AMR) AF: 0.560 AC: 8560 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2105 AN: 5148

South Asian (SAS) AF: 0.562 AC: 2710 AN: 4820

European-Finnish (FIN) AF: 0.503 AC: 5312 AN: 10560

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34075 AN: 67966

Other (OTH) AF: 0.438 AC: 927 AN: 2116

Alfa AF: 0.492 Hom.: 25518

Bravo AF: 0.429

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.64
PhyloP100		0.20
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: rs9640666; hg19: chr7-101032269;