2-36850952-A-AT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003162.4(STRN):c.2086+47_2086+48insA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (15046 hom., cov: 0)
  • Exomes 𝑓: 0.45 (11302 hom.)
  • Failed GnomAD Quality Control
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.369

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 -10 ACMG points.

• BP6: Variant 2-36850952-A-AT is Benign according to our data. Variant chr2-36850952-A-AT is described in ClinVar as [Benign]. Clinvar id is 1229283.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN	NM_003162.4	c.2086+47_2086+48insA		intron_variant		ENST00000263918.9
STRN	XM_005264519.6	c.1975+47_1975+48insA		intron_variant
STRN	XM_011533073.3	c.2173+47_2173+48insA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN	ENST00000263918.9	c.2086+47_2086+48insA		intron_variant		1	NM_003162.4	P1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 65628 AN: 147712 Hom.: 15049 Cov.: 0

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.464

GnomAD3 exomes AF: 0.449 AC: 60158 AN: 133908 Hom.: 2262 AF XY: 0.449 AC XY: 33252 AN XY: 74084

Gnomad AFR exome AF: 0.343

Gnomad AMR exome AF: 0.467

Gnomad ASJ exome AF: 0.456

Gnomad EAS exome AF: 0.388

Gnomad SAS exome AF: 0.420

Gnomad FIN exome AF: 0.459

Gnomad NFE exome AF: 0.472

Gnomad OTH exome AF: 0.460

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.447 AC: 473119 AN: 1059300 Hom.: 11302 Cov.: 19 AF XY: 0.445 AC XY: 236707 AN XY: 531466

Gnomad4 AFR exome AF: 0.302

Gnomad4 AMR exome AF: 0.450

Gnomad4 ASJ exome AF: 0.444

Gnomad4 EAS exome AF: 0.396

Gnomad4 SAS exome AF: 0.400

Gnomad4 FIN exome AF: 0.441

Gnomad4 NFE exome AF: 0.457

Gnomad4 OTH exome AF: 0.434

GnomAD4 genome AF: 0.444 AC: 65625 AN: 147786 Hom.: 15046 Cov.: 0 AF XY: 0.439 AC XY: 31499 AN XY: 71778

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.461

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

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: rs10668550; hg19: chr2-37078095;