rs6947185

Variant names:

• chr7-101398477-C-A
• rs6947185
• NM_001278563.3:c.159-21500C>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.159-21500C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,954 control chromosomes in the GnomAD database, including 32,555 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 0.65 (32555 hom., cov: 32)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.67 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL26A1	NM_001278563.3	MANE Select	c.159-21500C>A		intron	N/A	NP_001265492.1
	COL26A1	NM_133457.5		c.159-21500C>A		intron	N/A	NP_597714.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL26A1	ENST00000313669.12	TSL:1 MANE Select	c.159-21500C>A		intron	N/A	ENSP00000318234.8
	COL26A1	ENST00000613501.1	TSL:1	c.159-21500C>A		intron	N/A	ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99187 AN: 151836 Hom.: 32540 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.653 AC: 99243 AN: 151954 Hom.: 32555 Cov.: 32 AF XY: 0.651 AC XY: 48319 AN XY: 74242

African (AFR) AF: 0.643 AC: 26650 AN: 41436

American (AMR) AF: 0.681 AC: 10375 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2186 AN: 3466

East Asian (EAS) AF: 0.506 AC: 2606 AN: 5154

South Asian (SAS) AF: 0.655 AC: 3155 AN: 4814

European-Finnish (FIN) AF: 0.648 AC: 6833 AN: 10550

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45198 AN: 67980

Other (OTH) AF: 0.642 AC: 1352 AN: 2106

Alfa AF: 0.668 Hom.: 20048

Bravo AF: 0.654

Asia WGS AF: 0.583 AC: 2028 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.63
PhyloP100		-0.65
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: rs6947185; hg19: chr7-101041758;