2-36857574-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003162.4(STRN):​c.1837+282A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 151,908 control chromosomes in the GnomAD database, including 61,793 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.89 ( 61793 hom., cov: 28)

Consequence

STRN
NM_003162.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.94
Variant links:
Genes affected
STRN (HGNC:11424): (striatin) Enables armadillo repeat domain binding activity; estrogen receptor binding activity; and protein phosphatase 2A binding activity. Involved in Wnt signaling pathway and negative regulation of cell population proliferation. Located in bicellular tight junction. Part of FAR/SIN/STRIPAK complex. [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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BP6
Variant 2-36857574-T-C is Benign according to our data. Variant chr2-36857574-T-C is described in ClinVar as [Benign]. Clinvar id is 1282192.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STRNNM_003162.4 linkc.1837+282A>G intron_variant Intron 14 of 17 ENST00000263918.9 NP_003153.2 O43815-1
STRNXM_011533073.3 linkc.1924+282A>G intron_variant Intron 15 of 18 XP_011531375.1
STRNXM_005264519.6 linkc.1726+282A>G intron_variant Intron 13 of 16 XP_005264576.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STRNENST00000263918.9 linkc.1837+282A>G intron_variant Intron 14 of 17 1 NM_003162.4 ENSP00000263918.4 O43815-1

Frequencies

GnomAD3 genomes
AF:
0.894
AC:
135732
AN:
151790
Hom.:
61761
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.710
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.950
Gnomad ASJ
AF:
0.970
Gnomad EAS
AF:
0.873
Gnomad SAS
AF:
0.905
Gnomad FIN
AF:
0.969
Gnomad MID
AF:
0.943
Gnomad NFE
AF:
0.976
Gnomad OTH
AF:
0.906
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.894
AC:
135809
AN:
151908
Hom.:
61793
Cov.:
28
AF XY:
0.895
AC XY:
66460
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.710
Gnomad4 AMR
AF:
0.950
Gnomad4 ASJ
AF:
0.970
Gnomad4 EAS
AF:
0.874
Gnomad4 SAS
AF:
0.907
Gnomad4 FIN
AF:
0.969
Gnomad4 NFE
AF:
0.976
Gnomad4 OTH
AF:
0.907
Alfa
AF:
0.934
Hom.:
3336
Bravo
AF:
0.884
Asia WGS
AF:
0.871
AC:
3028
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.24
DANN
Benign
0.12

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: rs2717496; hg19: chr2-37084717; API