rs2903308

Variant names:

• chr16-13563028-A-G
• rs2903308
• ENST00000655174.1:n.855A>G

Variant summary

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

The ENST00000655174.1(ENSG00000262801):​n.855A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,144 control chromosomes in the GnomAD database, including 24,557 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 0.56 (24555 hom., cov: 33)
  • Exomes 𝑓: 0.70 (2 hom.)
• Consequence: ENSG00000262801 ENST00000655174.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

ENSG00000262801 (HGNC:):

SHISA9 (HGNC:37231): (shisa family member 9) Predicted to enable PDZ domain binding activity. Predicted to be involved in regulation of AMPA receptor activity and regulation of short-term neuronal synaptic plasticity. Predicted to be located in synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in glutamatergic synapse; postsynaptic density; and synaptic membrane. Predicted to be integral component of postsynaptic density membrane. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	XR_932915.3	n.*11A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262801	ENST00000655174.1	n.855A>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000262801	ENST00000571619.5	n.*110A>G		downstream_gene_variant		3
ENSG00000262801	ENST00000574540.2	n.*16A>G		downstream_gene_variant		3
ENSG00000262801	ENST00000653029.1	n.*16A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84771 AN: 152016 Hom.: 24522 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.546

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 2 AF XY: 0.833 AC XY: 5 AN XY: 6

Gnomad4 FIN exome AF: 0.700

GnomAD4 genome AF: 0.558 AC: 84856 AN: 152134 Hom.: 24555 Cov.: 33 AF XY: 0.560 AC XY: 41680 AN XY: 74368

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.544

Alfa AF: 0.490 Hom.: 31629

Bravo AF: 0.581

Asia WGS AF: 0.695 AC: 2418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2903308; hg19: chr16-13656885;