rs2540923

Variant names:

• chr2-36867802-A-C
• rs2540923
• NM_003162.4:c.1547+12T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-36867802-A-C
• chr2-36867802-A-G
• chr2-36867802-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003162.4(STRN):​c.1547+12T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000724 in 1,380,336 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 17 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STRN	NM_003162.4	c.1547+12T>G		intron_variant	Intron 12 of 17	ENST00000263918.9	NP_003153.2
STRN	XM_011533073.3	c.1634+12T>G		intron_variant	Intron 13 of 18		XP_011531375.1
STRN	XM_005264519.6	c.1436+12T>G		intron_variant	Intron 11 of 16		XP_005264576.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STRN	ENST00000263918.9	c.1547+12T>G		intron_variant	Intron 12 of 17	1	NM_003162.4	ENSP00000263918.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.24e-7 AC: 1 AN: 1380336 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 687760

African (AFR) AF: 0.00 AC: 0 AN: 29966

American (AMR) AF: 0.00 AC: 0 AN: 34680

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24158

East Asian (EAS) AF: 0.00 AC: 0 AN: 36944

South Asian (SAS) AF: 0.00 AC: 0 AN: 74946

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50840

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5514

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1066310

Other (OTH) AF: 0.0000176 AC: 1 AN: 56978

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.49
DANN	Benign	0.84
PhyloP100		-1.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2540923; hg19: chr2-37094945;