16-13483947-T-C

Variant names:

• chr16-13483947-T-C
• rs12708772
• ENST00000571619.5:n.552+9606T>C

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.552+9606T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,934 control chromosomes in the GnomAD database, including 24,700 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 (24700 hom., cov: 32)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000571619.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262801	ENST00000571619.5	TSL:3	n.552+9606T>C		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.726+9606T>C		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.533+9606T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85363 AN: 151816 Hom.: 24682 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.562 AC: 85406 AN: 151934 Hom.: 24700 Cov.: 32 AF XY: 0.568 AC XY: 42169 AN XY: 74212

African (AFR) AF: 0.453 AC: 18764 AN: 41408

American (AMR) AF: 0.711 AC: 10853 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3878 AN: 5152

South Asian (SAS) AF: 0.690 AC: 3323 AN: 4816

European-Finnish (FIN) AF: 0.542 AC: 5720 AN: 10548

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38849 AN: 67954

Other (OTH) AF: 0.616 AC: 1299 AN: 2108

Alfa AF: 0.577 Hom.: 42976

Bravo AF: 0.571

Asia WGS AF: 0.697 AC: 2419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.27
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12708772;

hg19: chr16-13577804;