chr2-36963249-G-C

Variant names:

• chr2-36963249-G-C
• rs11685600
• NM_003162.4:c.234+2981C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003162.4(STRN):​c.234+2981C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,254 control chromosomes in the GnomAD database, including 692 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.077 (692 hom., cov: 32)
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 0 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN	NM_003162.4	MANE Select	c.234+2981C>G		intron	N/A	NP_003153.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN	ENST00000263918.9	TSL:1 MANE Select	c.234+2981C>G		intron	N/A	ENSP00000263918.4

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11717 AN: 152138 Hom.: 678 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0402

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0772 AC: 11755 AN: 152254 Hom.: 692 Cov.: 32 AF XY: 0.0773 AC XY: 5755 AN XY: 74436

African (AFR) AF: 0.160 AC: 6650 AN: 41526

American (AMR) AF: 0.0402 AC: 615 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.128 AC: 661 AN: 5184

South Asian (SAS) AF: 0.0985 AC: 476 AN: 4832

European-Finnish (FIN) AF: 0.0539 AC: 572 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0361 AC: 2455 AN: 68030

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0154 Hom.: 7

Bravo AF: 0.0804

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.63
PhyloP100		0.034
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: rs11685600; hg19: chr2-37190392;