rs1025412

Variant summary

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

The NM_006108.4(SPON1):​c.826-18582G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 499,704 control chromosomes in the GnomAD database, including 67,987 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 0.51 ( 20326 hom., cov: 31)
Exomes 𝑓: 0.52 ( 47661 hom. )

Consequence

SPON1
NM_006108.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.635
Variant links:
Genes affected
SPON1 (HGNC:11252): (spondin 1) Predicted to be an extracellular matrix structural constituent. Predicted to be involved in cell adhesion. Predicted to act upstream of or within positive regulation of protein binding activity; positive regulation of protein processing; and regulation of amyloid precursor protein catabolic process. Located in extracellular space. Colocalizes with collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SPON1NM_006108.4 linkuse as main transcriptc.826-18582G>A intron_variant ENST00000576479.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SPON1ENST00000576479.4 linkuse as main transcriptc.826-18582G>A intron_variant 1 NM_006108.4 P1

Frequencies

GnomAD3 genomes
AF:
0.514
AC:
78114
AN:
151886
Hom.:
20324
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.501
Gnomad AMI
AF:
0.786
Gnomad AMR
AF:
0.445
Gnomad ASJ
AF:
0.416
Gnomad EAS
AF:
0.632
Gnomad SAS
AF:
0.591
Gnomad FIN
AF:
0.493
Gnomad MID
AF:
0.462
Gnomad NFE
AF:
0.529
Gnomad OTH
AF:
0.500
GnomAD3 exomes
AF:
0.510
AC:
110327
AN:
216250
Hom.:
28952
AF XY:
0.518
AC XY:
61845
AN XY:
119284
show subpopulations
Gnomad AFR exome
AF:
0.501
Gnomad AMR exome
AF:
0.395
Gnomad ASJ exome
AF:
0.405
Gnomad EAS exome
AF:
0.621
Gnomad SAS exome
AF:
0.575
Gnomad FIN exome
AF:
0.488
Gnomad NFE exome
AF:
0.524
Gnomad OTH exome
AF:
0.498
GnomAD4 exome
AF:
0.517
AC:
179595
AN:
347700
Hom.:
47661
Cov.:
0
AF XY:
0.526
AC XY:
104959
AN XY:
199450
show subpopulations
Gnomad4 AFR exome
AF:
0.499
Gnomad4 AMR exome
AF:
0.396
Gnomad4 ASJ exome
AF:
0.405
Gnomad4 EAS exome
AF:
0.621
Gnomad4 SAS exome
AF:
0.575
Gnomad4 FIN exome
AF:
0.494
Gnomad4 NFE exome
AF:
0.524
Gnomad4 OTH exome
AF:
0.514
GnomAD4 genome
AF:
0.514
AC:
78153
AN:
152004
Hom.:
20326
Cov.:
31
AF XY:
0.515
AC XY:
38260
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.501
Gnomad4 AMR
AF:
0.444
Gnomad4 ASJ
AF:
0.416
Gnomad4 EAS
AF:
0.632
Gnomad4 SAS
AF:
0.590
Gnomad4 FIN
AF:
0.493
Gnomad4 NFE
AF:
0.529
Gnomad4 OTH
AF:
0.498
Alfa
AF:
0.523
Hom.:
48643
Bravo
AF:
0.511
Asia WGS
AF:
0.544
AC:
1891
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.54
DANN
Benign
0.67

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: rs1025412; hg19: chr11-14246296; COSMIC: COSV59958291; API