2-36857574-T-C

Variant names:

• chr2-36857574-T-C
• rs2717496
• NM_003162.4:c.1837+282A>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.94

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]

ACMG classification

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
STRN	NM_003162.4	c.1837+282A>G		intron_variant	Intron 14 of 17	ENST00000263918.9	NP_003153.2
STRN	XM_011533073.3	c.1924+282A>G		intron_variant	Intron 15 of 18		XP_011531375.1
STRN	XM_005264519.6	c.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
STRN	ENST00000263918.9	c.1837+282A>G		intron_variant	Intron 14 of 17	1	NM_003162.4	ENSP00000263918.4

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135732 AN: 151790 Hom.: 61761 Cov.: 28

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

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

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

Other links and lift over

dbSNP: rs2717496; hg19: chr2-37084717;