2-36867661-C-T

Position:

• chr2-36867661-C-T

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.1547+153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,034 control chromosomes in the GnomAD database, including 165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.038 (165 hom., cov: 32)
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.871

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=-0.85).
• BP6: Variant 2-36867661-C-T is Benign according to our data. Variant chr2-36867661-C-T is described in ClinVar as [Benign]. Clinvar id is 1231795.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN	NM_003162.4	c.1547+153G>A		intron_variant		ENST00000263918.9
STRN	XM_005264519.6	c.1436+153G>A		intron_variant
STRN	XM_011533073.3	c.1634+153G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN	ENST00000263918.9	c.1547+153G>A		intron_variant		1	NM_003162.4	P1

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5743 AN: 151916 Hom.: 164 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0231

Gnomad OTH AF: 0.0497

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0378 AC: 5743 AN: 152034 Hom.: 165 Cov.: 32 AF XY: 0.0384 AC XY: 2854 AN XY: 74308

Gnomad4 AFR AF: 0.0535

Gnomad4 AMR AF: 0.0198

Gnomad4 ASJ AF: 0.0289

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0918

Gnomad4 FIN AF: 0.0314

Gnomad4 NFE AF: 0.0231

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0295 Hom.: 17

Bravo AF: 0.0371

Asia WGS AF: 0.110 AC: 380 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.46
DANN	Benign	0.93

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: rs75915538; hg19: chr2-37094804;