NM_003162.4:c.1838-200G>A

Variant names:

• chr2-36855552-C-T
• rs998321
• NM_003162.4:c.1838-200G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003162.4(STRN):​c.1838-200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,176 control chromosomes in the GnomAD database, including 56,753 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.85 (56753 hom., cov: 32)
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.656
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 2-36855552-C-T is Benign according to our data. Variant chr2-36855552-C-T is described in ClinVar as Benign. ClinVar VariationId is 1237891.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003162.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN	NM_003162.4	MANE Select	c.1838-200G>A		intron	N/A	NP_003153.2	O43815-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN	ENST00000263918.9	TSL:1 MANE Select	c.1838-200G>A		intron	N/A	ENSP00000263918.4	O43815-1
	STRN	ENST00000950120.1		c.1982-200G>A		intron	N/A	ENSP00000620179.1
	STRN	ENST00000874612.1		c.1925-200G>A		intron	N/A	ENSP00000544671.1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129014 AN: 152060 Hom.: 56725 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.848 AC: 129081 AN: 152176 Hom.: 56753 Cov.: 32 AF XY: 0.851 AC XY: 63293 AN XY: 74406

African (AFR) AF: 0.592 AC: 24538 AN: 41444

American (AMR) AF: 0.928 AC: 14204 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3357 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4521 AN: 5188

South Asian (SAS) AF: 0.891 AC: 4298 AN: 4822

European-Finnish (FIN) AF: 0.939 AC: 9965 AN: 10614

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65229 AN: 68012

Other (OTH) AF: 0.877 AC: 1855 AN: 2114

Alfa AF: 0.914 Hom.: 32956

Bravo AF: 0.834

Asia WGS AF: 0.856 AC: 2973 AN: 3470

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs998321; hg19: chr2-37082695;