16-13160099-G-T

Variant names:

• chr16-13160099-G-T
• rs153091
• NM_001145204.3:c.692-43295G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145204.3(SHISA9):​c.692-43295G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,090 control chromosomes in the GnomAD database, including 44,936 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 0.77 (44936 hom., cov: 32)
• Consequence: SHISA9 NM_001145204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 7 publications found

Genes affected

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145204.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHISA9	NM_001145204.3	MANE Select	c.692-43295G>T		intron	N/A	NP_001138676.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHISA9	ENST00000558583.3	TSL:5 MANE Select	c.692-43295G>T		intron	N/A	ENSP00000454014.2
	SHISA9	ENST00000566106.1	TSL:4	n.136-43295G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116709 AN: 151972 Hom.: 44900 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.768 AC: 116803 AN: 152090 Hom.: 44936 Cov.: 32 AF XY: 0.769 AC XY: 57139 AN XY: 74342

African (AFR) AF: 0.738 AC: 30644 AN: 41510

American (AMR) AF: 0.803 AC: 12278 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2816 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4529 AN: 5170

South Asian (SAS) AF: 0.803 AC: 3877 AN: 4826

European-Finnish (FIN) AF: 0.715 AC: 7551 AN: 10568

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.775 AC: 52670 AN: 67940

Other (OTH) AF: 0.802 AC: 1694 AN: 2112

Alfa AF: 0.779 Hom.: 212600

Bravo AF: 0.771

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.27
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

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: rs153091; hg19: chr16-13253956;