rs11156654

Positions:

• chr14-31014749-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001083893.2(STRN3):​c.282+11155A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 441,822 control chromosomes in the GnomAD database, including 13,059 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 0.25 (5002 hom., cov: 29)
  • Exomes 𝑓: 0.22 (8057 hom.)
• Consequence: STRN3 NM_001083893.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

STRN3 (HGNC:15720): (striatin 3) Enables armadillo repeat domain binding activity; protein phosphatase 2A binding activity; and small GTPase binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in Golgi apparatus; nucleoplasm; and plasma membrane. Part of FAR/SIN/STRIPAK complex. [provided by Alliance of Genome Resources, Apr 2022]

MIR624 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRN3	NM_001083893.2	c.282+11155A>T		intron_variant		ENST00000357479.10	NP_001077362.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRN3	ENST00000357479.10	c.282+11155A>T		intron_variant		5	NM_001083893.2	ENSP00000350071.5
STRN3	ENST00000355683.9	c.282+11155A>T		intron_variant		1		ENSP00000347909.5
STRN3	ENST00000555358.5	n.282+11155A>T		intron_variant		1		ENSP00000451028.1
MIR624	ENST00000385217.1	n.-7A>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37811 AN: 151436 Hom.: 5001 Cov.: 29

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.235

GnomAD3 exomes AF: 0.204 AC: 26296 AN: 129210 Hom.: 3086 AF XY: 0.201 AC XY: 13793 AN XY: 68558

Gnomad AFR exome AF: 0.292

Gnomad AMR exome AF: 0.122

Gnomad ASJ exome AF: 0.223

Gnomad EAS exome AF: 0.00140

Gnomad SAS exome AF: 0.148

Gnomad FIN exome AF: 0.262

Gnomad NFE exome AF: 0.248

Gnomad OTH exome AF: 0.219

GnomAD4 exome AF: 0.222 AC: 64583 AN: 290270 Hom.: 8057 Cov.: 0 AF XY: 0.218 AC XY: 36073 AN XY: 165456

Gnomad4 AFR exome AF: 0.275

Gnomad4 AMR exome AF: 0.116

Gnomad4 ASJ exome AF: 0.227

Gnomad4 EAS exome AF: 0.00101

Gnomad4 SAS exome AF: 0.157

Gnomad4 FIN exome AF: 0.264

Gnomad4 NFE exome AF: 0.260

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.250 AC: 37826 AN: 151552 Hom.: 5002 Cov.: 29 AF XY: 0.246 AC XY: 18191 AN XY: 74040

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.232

Alfa AF: 0.258 Hom.: 1690

Bravo AF: 0.243

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs11156654; hg19: chr14-31483955; COSMIC: COSV62581230; COSMIC: COSV62581230;