11-70470286-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_012309.5(SHANK2):c.*2583T>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 0.273 in 152,310 control chromosomes in the GnomAD database, including 6,312 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.27 (6308 hom., cov: 33)
  • Exomes 𝑓: 0.34 (4 hom.)
• Consequence: SHANK2 NM_012309.5 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.266

Genes affected

SHANK2 (HGNC:14295): (SH3 and multiple ankyrin repeat domains 2) This gene encodes a protein that is a member of the Shank family of synaptic proteins that may function as molecular scaffolds in the postsynaptic density of excitatory synapses. Shank proteins contain multiple domains for protein-protein interaction, including ankyrin repeats, and an SH3 domain. This particular family member contains a PDZ domain, a consensus sequence for cortactin SH3 domain-binding peptides and a sterile alpha motif. The alternative splicing demonstrated in Shank genes has been suggested as a mechanism for regulating the molecular structure of Shank and the spectrum of Shank-interacting proteins in the postsynaptic densities of the adult and developing brain. Alterations in the encoded protein may be associated with susceptibility to autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 11-70470286-A-G is Benign according to our data. Variant chr11-70470286-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 305889.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHANK2	NM_012309.5	c.*2583T>C		3_prime_UTR_variant	26/26	ENST00000601538.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHANK2	ENST00000601538.6	c.*2583T>C		3_prime_UTR_variant	26/26	5	NM_012309.5	P1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41491 AN: 152124 Hom.: 6302 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.338 AC: 23 AN: 68 Hom.: 4 Cov.: 0 AF XY: 0.316 AC XY: 12 AN XY: 38

Gnomad4 FIN exome AF: 0.355

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.273 AC: 41494 AN: 152242 Hom.: 6308 Cov.: 33 AF XY: 0.272 AC XY: 20235 AN XY: 74446

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.293

Alfa AF: 0.298 Hom.: 1617

Bravo AF: 0.269

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Autism spectrum disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.32
Dann	Benign	0.47

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: rs55678639; hg19: chr11-70316391;