19-46724564-G-A

Variant names:

• chr19-46724564-G-A
• rs11668987
• NM_013403.3:c.1594+243C>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.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
• Publications: 14 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN4	NM_013403.3	MANE Select	c.1594+243C>T		intron	N/A	NP_037535.2
	STRN4	NM_001039877.2		c.1615+243C>T		intron	N/A	NP_001034966.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRN4	ENST00000263280.11	TSL:1 MANE Select	c.1594+243C>T		intron	N/A	ENSP00000263280.4
	STRN4	ENST00000391910.7	TSL:5	c.1615+243C>T		intron	N/A	ENSP00000375777.1
	STRN4	ENST00000539396.5	TSL:2	c.1237+243C>T		intron	N/A	ENSP00000440901.1

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

African (AFR) AF: 0.137 AC: 5672 AN: 41536

American (AMR) AF: 0.202 AC: 3085 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 963 AN: 3472

East Asian (EAS) AF: 0.0558 AC: 289 AN: 5178

South Asian (SAS) AF: 0.199 AC: 961 AN: 4830

European-Finnish (FIN) AF: 0.188 AC: 1997 AN: 10602

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

European-Non Finnish (NFE) AF: 0.238 AC: 16206 AN: 67996

Other (OTH) AF: 0.228 AC: 481 AN: 2112

Alfa AF: 0.217 Hom.: 1600

Bravo AF: 0.193

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		0.14
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11668987; hg19: chr19-47227821;