rs11685600

chr2-36963249-G-Cchr2-36963249-G-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN	NM_003162.4	c.234+2981C>G		intron_variant		ENST00000263918.9
STRN	XM_005264519.6	c.234+2981C>G		intron_variant
STRN	XM_011533073.3	c.234+2981C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN	ENST00000263918.9	c.234+2981C>G		intron_variant		1	NM_003162.4	P1

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

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0402

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0985

Gnomad4 FIN AF: 0.0539

Gnomad4 NFE AF: 0.0361

Gnomad4 OTH AF: 0.0696

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	15
Dann	Benign	0.63

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: rs11685600; hg19: chr2-37190392;