3-136672353-A-G

Variant summary

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

The NM_005862.3(STAG1):​c.-83-41372T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,230 control chromosomes in the GnomAD database, including 6,361 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 0.29 ( 6361 hom., cov: 32)

Consequence

STAG1
NM_005862.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.01
Variant links:
Genes affected
STAG1 (HGNC:11354): (STAG1 cohesin complex component) This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008]

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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STAG1NM_005862.3 linkc.-83-41372T>C intron_variant Intron 1 of 33 ENST00000383202.7 NP_005853.2 Q8WVM7-1Q4LE48
STAG1XR_001739978.2 linkn.185-41372T>C intron_variant Intron 1 of 23

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STAG1ENST00000383202.7 linkc.-83-41372T>C intron_variant Intron 1 of 33 1 NM_005862.3 ENSP00000372689.2 Q8WVM7-1

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
43773
AN:
152112
Hom.:
6355
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.319
Gnomad AMI
AF:
0.409
Gnomad AMR
AF:
0.263
Gnomad ASJ
AF:
0.360
Gnomad EAS
AF:
0.137
Gnomad SAS
AF:
0.199
Gnomad FIN
AF:
0.278
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.287
Gnomad OTH
AF:
0.307
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.288
AC:
43801
AN:
152230
Hom.:
6361
Cov.:
32
AF XY:
0.287
AC XY:
21330
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.319
Gnomad4 AMR
AF:
0.263
Gnomad4 ASJ
AF:
0.360
Gnomad4 EAS
AF:
0.136
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.278
Gnomad4 NFE
AF:
0.287
Gnomad4 OTH
AF:
0.304
Alfa
AF:
0.264
Hom.:
2805
Bravo
AF:
0.289
Asia WGS
AF:
0.177
AC:
618
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
6.1
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: rs3856637; hg19: chr3-136391195; API