rs4802322

Positions:

• chr19-46739735-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.283-847C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,074 control chromosomes in the GnomAD database, including 5,695 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 0.27 (5695 hom., cov: 32)
• Consequence: STRN4 NM_013403.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN4	NM_013403.3	c.283-847C>T		intron_variant		ENST00000263280.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN4	ENST00000263280.11	c.283-847C>T		intron_variant		1	NM_013403.3	P4

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40320 AN: 151956 Hom.: 5684 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.265 AC: 40354 AN: 152074 Hom.: 5695 Cov.: 32 AF XY: 0.264 AC XY: 19617 AN XY: 74342

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0877

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.283

Alfa AF: 0.247 Hom.: 4821

Bravo AF: 0.269

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs4802322; hg19: chr19-47242992;