rs407146

Variant names:

• chr16-13221798-C-A
• rs407146
• NM_001145204.3:c.895+8498C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-13221798-C-A
• chr16-13221798-C-G

Variant summary

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

The NM_001145204.3(SHISA9):​c.895+8498C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,918 control chromosomes in the GnomAD database, including 17,744 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 0.47 (17744 hom., cov: 32)
• Consequence: SHISA9 NM_001145204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	NM_001145204.3	c.895+8498C>A		intron_variant	Intron 4 of 4	ENST00000558583.3	NP_001138676.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHISA9	ENST00000558583.3	c.895+8498C>A		intron_variant	Intron 4 of 4	5	NM_001145204.3	ENSP00000454014.2
SHISA9	ENST00000566106.1	n.292-13232C>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71630 AN: 151800 Hom.: 17699 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.472 AC: 71719 AN: 151918 Hom.: 17744 Cov.: 32 AF XY: 0.479 AC XY: 35518 AN XY: 74210

African (AFR) AF: 0.584 AC: 24188 AN: 41430

American (AMR) AF: 0.540 AC: 8245 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1382 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3866 AN: 5142

South Asian (SAS) AF: 0.520 AC: 2500 AN: 4812

European-Finnish (FIN) AF: 0.414 AC: 4366 AN: 10534

Middle Eastern (MID) AF: 0.390 AC: 113 AN: 290

European-Non Finnish (NFE) AF: 0.378 AC: 25701 AN: 67952

Other (OTH) AF: 0.448 AC: 942 AN: 2104

Alfa AF: 0.381 Hom.: 5719

Bravo AF: 0.490

Asia WGS AF: 0.624 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.39
PhyloP100		0.44
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: rs407146; hg19: chr16-13315655;