7-101388988-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001278563.3(COL26A1):​c.158+25798G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 138052 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 85724

African (AFR) AF: 0.00 AC: 0 AN: 2908

American (AMR) AF: 0.00 AC: 0 AN: 10258

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2838

East Asian (EAS) AF: 0.00 AC: 0 AN: 5206

South Asian (SAS) AF: 0.00 AC: 0 AN: 20748

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 404

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 81888

Other (OTH) AF: 0.00 AC: 0 AN: 6184

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 25518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.31
DANN	Benign	0.67
PhyloP100		0.20

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;