2-36849872-C-A

Variant names:

• chr2-36849872-C-A
• rs723674
• NM_003162.4:c.2087-72G>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003162.4(STRN):​c.2087-72G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.989 in 1,464,934 control chromosomes in the GnomAD database, including 718,280 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.95 (68640 hom., cov: 31)
  • Exomes 𝑓: 0.99 (649640 hom.)
• Consequence: STRN NM_003162.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.175

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 2-36849872-C-A is Benign according to our data. Variant chr2-36849872-C-A is described in ClinVar as [Benign]. Clinvar id is 1249083.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STRN	NM_003162.4	c.2087-72G>T		intron_variant	Intron 16 of 17	ENST00000263918.9	NP_003153.2
STRN	XM_011533073.3	c.2174-72G>T		intron_variant	Intron 17 of 18		XP_011531375.1
STRN	XM_005264519.6	c.1976-72G>T		intron_variant	Intron 15 of 16		XP_005264576.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STRN	ENST00000263918.9	c.2087-72G>T		intron_variant	Intron 16 of 17	1	NM_003162.4	ENSP00000263918.4

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143918 AN: 152168 Hom.: 68586 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.959

GnomAD4 exome AF: 0.994 AC: 1305335 AN: 1312648 Hom.: 649640 AF XY: 0.995 AC XY: 658203 AN XY: 661296

Gnomad4 AFR exome AF: 0.810

Gnomad4 AMR exome AF: 0.989

Gnomad4 ASJ exome AF: 0.999

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.988

GnomAD4 genome AF: 0.946 AC: 144033 AN: 152286 Hom.: 68640 Cov.: 31 AF XY: 0.948 AC XY: 70555 AN XY: 74462

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.978

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.999

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.999

Gnomad4 OTH AF: 0.959

Alfa AF: 0.977 Hom.: 14469

Bravo AF: 0.937

Asia WGS AF: 0.988 AC: 3436 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

May 15, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.53
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs723674; hg19: chr2-37077015;