16-13527425-T-C

Variant names:

• chr16-13527425-T-C
• rs10492775
• ENST00000571619.5:n.553-35282T>C

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.553-35282T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0822 in 152,192 control chromosomes in the GnomAD database, including 574 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 0.082 (574 hom., cov: 32)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262801	ENST00000571619.5	TSL:3	n.553-35282T>C		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.727-35282T>C		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.534-24968T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12498 AN: 152074 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0822 AC: 12509 AN: 152192 Hom.: 574 Cov.: 32 AF XY: 0.0838 AC XY: 6237 AN XY: 74398

African (AFR) AF: 0.0549 AC: 2279 AN: 41548

American (AMR) AF: 0.162 AC: 2472 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3472

East Asian (EAS) AF: 0.156 AC: 805 AN: 5176

South Asian (SAS) AF: 0.0934 AC: 449 AN: 4806

European-Finnish (FIN) AF: 0.0517 AC: 548 AN: 10606

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5403 AN: 67998

Other (OTH) AF: 0.0960 AC: 203 AN: 2114

Alfa AF: 0.0819 Hom.: 65

Bravo AF: 0.0901

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.32
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10492775; hg19: chr16-13621282;