rs11772003

Variant names:

• chr7-101400316-C-G
• rs11772003
• NM_001278563.3:c.159-19661C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-101400316-C-G
• chr7-101400316-C-T

Variant summary

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

The NM_001278563.3(COL26A1):​c.159-19661C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 150,278 control chromosomes in the GnomAD database, including 1,621 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 0.11 (1621 hom., cov: 29)
• Consequence: COL26A1 NM_001278563.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL26A1	NM_001278563.3	c.159-19661C>G		intron_variant	Intron 1 of 12	ENST00000313669.12	NP_001265492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL26A1	ENST00000313669.12	c.159-19661C>G		intron_variant	Intron 1 of 12	1	NM_001278563.3	ENSP00000318234.8
COL26A1	ENST00000613501.1	c.159-19661C>G		intron_variant	Intron 1 of 12	1		ENSP00000482102.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17048 AN: 150188 Hom.: 1603 Cov.: 29

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.0549

Gnomad MID AF: 0.0784

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.114 AC: 17108 AN: 150278 Hom.: 1621 Cov.: 29 AF XY: 0.113 AC XY: 8307 AN XY: 73280

African (AFR) AF: 0.259 AC: 10587 AN: 40800

American (AMR) AF: 0.0682 AC: 1025 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 234 AN: 3452

East Asian (EAS) AF: 0.109 AC: 555 AN: 5078

South Asian (SAS) AF: 0.0773 AC: 368 AN: 4760

European-Finnish (FIN) AF: 0.0549 AC: 557 AN: 10138

Middle Eastern (MID) AF: 0.0845 AC: 24 AN: 284

European-Non Finnish (NFE) AF: 0.0520 AC: 3522 AN: 67772

Other (OTH) AF: 0.104 AC: 214 AN: 2060

Alfa AF: 0.0311 Hom.: 32

Bravo AF: 0.122

Asia WGS AF: 0.104 AC: 363 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.80
PhyloP100		-0.31
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: rs11772003; hg19: chr7-101043597;