rs4802322

Variant names:

• chr19-46739735-G-A
• rs4802322
• NM_013403.3:c.283-847C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013403.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN4	NM_013403.3	MANE Select	c.283-847C>T		intron	N/A	NP_037535.2	Q9NRL3-1
	STRN4	NM_001039877.2		c.283-847C>T		intron	N/A	NP_001034966.1	Q9NRL3-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN4	ENST00000263280.11	TSL:1 MANE Select	c.283-847C>T		intron	N/A	ENSP00000263280.4	Q9NRL3-1
	STRN4	ENST00000391910.7	TSL:5	c.283-847C>T		intron	N/A	ENSP00000375777.1	Q9NRL3-3
	STRN4	ENST00000539396.5	TSL:2	c.-75-847C>T		intron	N/A	ENSP00000440901.1	F5GYK2

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

African (AFR) AF: 0.356 AC: 14774 AN: 41456

American (AMR) AF: 0.231 AC: 3525 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 956 AN: 3472

East Asian (EAS) AF: 0.0877 AC: 455 AN: 5186

South Asian (SAS) AF: 0.213 AC: 1027 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2361 AN: 10550

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16340 AN: 67982

Other (OTH) AF: 0.283 AC: 598 AN: 2116

Alfa AF: 0.251 Hom.: 6549

Bravo AF: 0.269

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.52
PhyloP100		0.30
PromoterAI		0.080	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4802322; hg19: chr19-47242992;