rs1230895

Variant names:

• chr16-13107581-G-A
• rs1230895
• NM_001145204.3:c.692-95813G>A

Variant summary

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

The NM_001145204.3(SHISA9):​c.692-95813G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,538 control chromosomes in the GnomAD database, including 3,351 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 0.20 (3351 hom., cov: 31)
• Consequence: SHISA9 NM_001145204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	NM_001145204.3	c.692-95813G>A		intron_variant	Intron 2 of 4	ENST00000558583.3	NP_001138676.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHISA9	ENST00000558583.3	c.692-95813G>A		intron_variant	Intron 2 of 4	5	NM_001145204.3	ENSP00000454014.2
SHISA9	ENST00000566106.1	n.135+25067G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30040 AN: 151420 Hom.: 3351 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.198 AC: 30042 AN: 151538 Hom.: 3351 Cov.: 31 AF XY: 0.196 AC XY: 14500 AN XY: 73990

African (AFR) AF: 0.108 AC: 4464 AN: 41318

American (AMR) AF: 0.190 AC: 2888 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1106 AN: 5152

South Asian (SAS) AF: 0.137 AC: 658 AN: 4804

European-Finnish (FIN) AF: 0.255 AC: 2653 AN: 10392

Middle Eastern (MID) AF: 0.153 AC: 44 AN: 288

European-Non Finnish (NFE) AF: 0.252 AC: 17088 AN: 67904

Other (OTH) AF: 0.212 AC: 447 AN: 2110

Alfa AF: 0.205 Hom.: 535

Bravo AF: 0.188

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.75
PhyloP100		2.8
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: rs1230895; hg19: chr16-13201438;