2-36838875-T-G

Position:

• chr2-36838875-T-G

Variant summary

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

The NM_003162.4(STRN):​c.*10581A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,960 control chromosomes in the GnomAD database, including 14,474 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 0.43 (14474 hom., cov: 32)
• Consequence: STRN NM_003162.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

Genes affected

STRN (HGNC:11424): (striatin) Enables armadillo repeat domain binding activity; estrogen receptor binding activity; and protein phosphatase 2A binding activity. Involved in Wnt signaling pathway and negative regulation of cell population proliferation. Located in bicellular tight junction. 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN	NM_003162.4	c.*10581A>C		3_prime_UTR_variant	18/18	ENST00000263918.9
STRN	XM_005264519.6	c.*10581A>C		3_prime_UTR_variant	17/17
STRN	XM_011533073.3	c.*10581A>C		3_prime_UTR_variant	19/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN	ENST00000263918.9	c.*10581A>C		3_prime_UTR_variant	18/18	1	NM_003162.4	P1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65685 AN: 151844 Hom.: 14454 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.433 AC: 65742 AN: 151960 Hom.: 14474 Cov.: 32 AF XY: 0.439 AC XY: 32574 AN XY: 74270

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.428

Alfa AF: 0.412 Hom.: 5225

Bravo AF: 0.420

Asia WGS AF: 0.512 AC: 1775 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1504; hg19: chr2-37066018;