chr16-13396523-A-C

Variant names:

• chr16-13396523-A-C
• rs734826
• ENST00000571619.5:n.420+46102A>C

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.420+46102A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,012 control chromosomes in the GnomAD database, including 32,557 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 0.65 (32557 hom., cov: 32)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 7 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262801	ENST00000571619.5	TSL:3	n.420+46102A>C		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.594+45907A>C		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.401+46102A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98145 AN: 151894 Hom.: 32510 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.646 AC: 98244 AN: 152012 Hom.: 32557 Cov.: 32 AF XY: 0.639 AC XY: 47484 AN XY: 74272

African (AFR) AF: 0.795 AC: 32967 AN: 41478

American (AMR) AF: 0.531 AC: 8098 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2307 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3175 AN: 5152

South Asian (SAS) AF: 0.691 AC: 3330 AN: 4818

European-Finnish (FIN) AF: 0.533 AC: 5628 AN: 10552

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40554 AN: 67974

Other (OTH) AF: 0.634 AC: 1340 AN: 2112

Alfa AF: 0.603 Hom.: 46733

Bravo AF: 0.648

Asia WGS AF: 0.684 AC: 2378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs734826; hg19: chr16-13490380;