chr7-101499248-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001278563.3(COL26A1):​c.386-33834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0924 in 152,192 control chromosomes in the GnomAD database, including 669 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 0.092 ( 669 hom., cov: 32)

Consequence

COL26A1
NM_001278563.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.378
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0941 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL26A1NM_001278563.3 linkuse as main transcriptc.386-33834A>G intron_variant ENST00000313669.12 NP_001265492.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL26A1ENST00000313669.12 linkuse as main transcriptc.386-33834A>G intron_variant 1 NM_001278563.3 ENSP00000318234 P4Q96A83-1
COL26A1ENST00000613501.1 linkuse as main transcriptc.380-33834A>G intron_variant 1 ENSP00000482102 A1Q96A83-2

Frequencies

GnomAD3 genomes
AF:
0.0923
AC:
14044
AN:
152074
Hom.:
668
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0842
Gnomad AMI
AF:
0.212
Gnomad AMR
AF:
0.0904
Gnomad ASJ
AF:
0.0844
Gnomad EAS
AF:
0.0944
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0908
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0961
Gnomad OTH
AF:
0.0942
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0924
AC:
14070
AN:
152192
Hom.:
669
Cov.:
32
AF XY:
0.0931
AC XY:
6926
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.0847
Gnomad4 AMR
AF:
0.0906
Gnomad4 ASJ
AF:
0.0844
Gnomad4 EAS
AF:
0.0938
Gnomad4 SAS
AF:
0.100
Gnomad4 FIN
AF:
0.0908
Gnomad4 NFE
AF:
0.0961
Gnomad4 OTH
AF:
0.0932
Alfa
AF:
0.0933
Hom.:
116
Bravo
AF:
0.0906
Asia WGS
AF:
0.111
AC:
387
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.6
DANN
Benign
0.73

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17135512; hg19: chr7-101142529; API