chr16-13264031-T-C

Variant names:

• chr16-13264031-T-C
• rs1468190
• ENST00000571619.5:n.178+5596T>C

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.178+5596T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,980 control chromosomes in the GnomAD database, including 32,502 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 (32502 hom., cov: 32)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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.178+5596T>C		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.157+17641T>C		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.159+17641T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98881 AN: 151862 Hom.: 32465 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.651 AC: 98969 AN: 151980 Hom.: 32502 Cov.: 32 AF XY: 0.653 AC XY: 48468 AN XY: 74258

African (AFR) AF: 0.720 AC: 29864 AN: 41450

American (AMR) AF: 0.689 AC: 10515 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3472

East Asian (EAS) AF: 0.444 AC: 2292 AN: 5162

South Asian (SAS) AF: 0.591 AC: 2847 AN: 4820

European-Finnish (FIN) AF: 0.677 AC: 7129 AN: 10534

Middle Eastern (MID) AF: 0.604 AC: 174 AN: 288

European-Non Finnish (NFE) AF: 0.622 AC: 42274 AN: 67964

Other (OTH) AF: 0.624 AC: 1314 AN: 2106

Alfa AF: 0.567 Hom.: 10234

Bravo AF: 0.659

Asia WGS AF: 0.557 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1468190; hg19: chr16-13357888;