chr2-36855099-TAA-T

Position:

• chr2-36855099-TAA-T

Variant summary

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

The NM_003162.4(STRN):​c.1978+111_1978+112del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 1,136,328 control chromosomes in the GnomAD database, including 4,751 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.067 (464 hom., cov: 31)
  • Exomes 𝑓: 0.090 (4287 hom.)
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.13

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 2-36855099-TAA-T is Benign according to our data. Variant chr2-36855099-TAA-T is described in ClinVar as [Benign]. Clinvar id is 1249221.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN	NM_003162.4	c.1978+111_1978+112del		intron_variant		ENST00000263918.9
STRN	XM_005264519.6	c.1867+111_1867+112del		intron_variant
STRN	XM_011533073.3	c.2065+111_2065+112del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN	ENST00000263918.9	c.1978+111_1978+112del		intron_variant		1	NM_003162.4	P1

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10142 AN: 152102 Hom.: 461 Cov.: 31

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.0742

GnomAD4 exome AF: 0.0896 AC: 88147 AN: 984108 Hom.: 4287 AF XY: 0.0907 AC XY: 44796 AN XY: 494088

Gnomad4 AFR exome AF: 0.0144

Gnomad4 AMR exome AF: 0.0991

Gnomad4 ASJ exome AF: 0.0587

Gnomad4 EAS exome AF: 0.00418

Gnomad4 SAS exome AF: 0.136

Gnomad4 FIN exome AF: 0.0884

Gnomad4 NFE exome AF: 0.0928

Gnomad4 OTH exome AF: 0.0864

GnomAD4 genome AF: 0.0667 AC: 10153 AN: 152220 Hom.: 464 Cov.: 31 AF XY: 0.0688 AC XY: 5122 AN XY: 74418

Gnomad4 AFR AF: 0.0175

Gnomad4 AMR AF: 0.0900

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0862

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.0749

Alfa AF: 0.0763 Hom.: 59

Bravo AF: 0.0635

Asia WGS AF: 0.0760 AC: 262 AN: 3476

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 16, 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: rs140276354; hg19: chr2-37082242;