chr16-13396523-A-C

Position:

• chr16-13396523-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047434582.1(SHISA9):​c.1212+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: SHISA9 XM_047434582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

Genes affected

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]

ENSG00000262801 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHISA9	XM_047434582.1	c.1212+46102A>C		intron_variant			XP_047290538.1
SHISA9	XM_011522642.3	c.1212+46102A>C		intron_variant			XP_011520944.1
SHISA9	XR_007064905.1	n.1556+46102A>C		intron_variant
SHISA9	XR_932915.3	n.1556+46102A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000262801	ENST00000571619.5	n.420+46102A>C		intron_variant		3
ENSG00000262801	ENST00000574540.2	n.594+45907A>C		intron_variant		3
ENSG00000262801	ENST00000653029.1	n.401+46102A>C		intron_variant

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

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.634

Alfa AF: 0.598 Hom.: 36607

Bravo AF: 0.648

Asia WGS AF: 0.684 AC: 2378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734826; hg19: chr16-13490380;