rs149917

Variant names:

• chr16-13144557-G-A
• rs149917
• NM_001145204.3:c.692-58837G>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.692-58837G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,944 control chromosomes in the GnomAD database, including 20,345 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 0.50 (20345 hom., cov: 31)
• Consequence: SHISA9 NM_001145204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	NM_001145204.3	c.692-58837G>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.692-58837G>A		intron_variant	Intron 2 of 4	5	NM_001145204.3	ENSP00000454014.2
SHISA9	ENST00000566106.1	n.136-58837G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75537 AN: 151828 Hom.: 20328 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.497 AC: 75573 AN: 151944 Hom.: 20345 Cov.: 31 AF XY: 0.499 AC XY: 37015 AN XY: 74248

African (AFR) AF: 0.283 AC: 11737 AN: 41448

American (AMR) AF: 0.571 AC: 8708 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2153 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2627 AN: 5162

South Asian (SAS) AF: 0.477 AC: 2292 AN: 4810

European-Finnish (FIN) AF: 0.625 AC: 6596 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39828 AN: 67934

Other (OTH) AF: 0.507 AC: 1068 AN: 2106

Alfa AF: 0.556 Hom.: 4327

Bravo AF: 0.486

Asia WGS AF: 0.449 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.30
DANN	Benign	0.60
PhyloP100		-1.9
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: rs149917; hg19: chr16-13238414;