chr16-13483947-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	XR_007064905.1	n.1688+9606T>C		intron_variant	Intron 5 of 6
SHISA9	XR_932915.3	n.1688+9606T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262801	ENST00000571619.5	n.552+9606T>C		intron_variant	Intron 4 of 4	3
ENSG00000262801	ENST00000574540.2	n.726+9606T>C		intron_variant	Intron 3 of 3	3
ENSG00000262801	ENST00000653029.1	n.533+9606T>C		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs12708772; hg19: chr16-13577804;