2-36850952-A-ATT

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+48insAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.42 (13311 hom., cov: 0)
  • Exomes 𝑓: 0.34 (7676 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-ATT is Benign according to our data. Variant chr2-36850952-A-ATT is described in ClinVar as [Benign]. Clinvar id is 1245944.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.423 AC: 62493 AN: 147818 Hom.: 13297 Cov.: 0

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.419

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.415

GnomAD3 exomes AF: 0.299 AC: 40089 AN: 133908 Hom.: 1247 AF XY: 0.300 AC XY: 22214 AN XY: 74084

Gnomad AFR exome AF: 0.234

Gnomad AMR exome AF: 0.272

Gnomad ASJ exome AF: 0.293

Gnomad EAS exome AF: 0.356

Gnomad SAS exome AF: 0.306

Gnomad FIN exome AF: 0.332

Gnomad NFE exome AF: 0.299

Gnomad OTH exome AF: 0.304

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.339 AC: 366550 AN: 1081156 Hom.: 7676 Cov.: 19 AF XY: 0.339 AC XY: 183631 AN XY: 542360

Gnomad4 AFR exome AF: 0.257

Gnomad4 AMR exome AF: 0.283

Gnomad4 ASJ exome AF: 0.336

Gnomad4 EAS exome AF: 0.393

Gnomad4 SAS exome AF: 0.348

Gnomad4 FIN exome AF: 0.347

Gnomad4 NFE exome AF: 0.340

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.423 AC: 62537 AN: 147894 Hom.: 13311 Cov.: 0 AF XY: 0.429 AC XY: 30830 AN XY: 71828

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.419

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

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Computational scores

Source: dbNSFP v4.3

Splicing

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;