rs11668987

chr19-46724564-G-A

Variant summary

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

The NM_013403.3(STRN4):c.1594+243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,234 control chromosomes in the GnomAD database, including 3,193 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 0.20 (3193 hom., cov: 33)
• Consequence: STRN4 NM_013403.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

Genes affected

STRN4 (HGNC:15721): (striatin 4) Enables armadillo repeat domain binding activity and protein phosphatase 2A binding activity. 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN4	NM_013403.3	c.1594+243C>T		intron_variant		ENST00000263280.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN4	ENST00000263280.11	c.1594+243C>T		intron_variant		1	NM_013403.3	P4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29956 AN: 152116 Hom.: 3187 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.197 AC: 29972 AN: 152234 Hom.: 3193 Cov.: 33 AF XY: 0.196 AC XY: 14620 AN XY: 74450

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.228

Alfa AF: 0.218 Hom.: 1279

Bravo AF: 0.193

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.1
Dann	Benign	0.42
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11668987; hg19: chr19-47227821;