16-13264031-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	XM_047434582.1	c.970+60482T>C		intron_variant	Intron 3 of 4		XP_047290538.1
SHISA9	XM_011522642.3	c.970+60482T>C		intron_variant	Intron 3 of 4		XP_011520944.1
LOC107984137	XR_001752087.2	n.262+5596T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262801	ENST00000571619.5	n.178+5596T>C		intron_variant	Intron 2 of 4	3
ENSG00000262801	ENST00000574540.2	n.157+17641T>C		intron_variant	Intron 1 of 3	3
ENSG00000262801	ENST00000653029.1	n.159+17641T>C		intron_variant	Intron 1 of 4

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 v4.3

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;