chr2-36854891-G-A

Position:

• chr2-36854891-G-A

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.1978+321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,118 control chromosomes in the GnomAD database, including 54,419 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.82 (54419 hom., cov: 33)
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.218

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=-0.64).
• BP6: Variant 2-36854891-G-A is Benign according to our data. Variant chr2-36854891-G-A is described in ClinVar as [Benign]. Clinvar id is 1258328.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN	NM_003162.4	c.1978+321C>T		intron_variant		ENST00000263918.9
STRN	XM_005264519.6	c.1867+321C>T		intron_variant
STRN	XM_011533073.3	c.2065+321C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN	ENST00000263918.9	c.1978+321C>T		intron_variant		1	NM_003162.4	P1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124873 AN: 152000 Hom.: 54397 Cov.: 33

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.821 AC: 124925 AN: 152118 Hom.: 54419 Cov.: 33 AF XY: 0.823 AC XY: 61263 AN XY: 74396

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.959

Gnomad4 OTH AF: 0.860

Alfa AF: 0.888 Hom.: 9305

Bravo AF: 0.803

Asia WGS AF: 0.852 AC: 2961 AN: 3472

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.93
DANN	Benign	0.43

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: rs1861433; hg19: chr2-37082034;