rs1858992

Variant names:

• chr16-13363817-C-T
• rs1858992
• ENST00000571619.5:n.420+13396C>T

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.420+13396C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,964 control chromosomes in the GnomAD database, including 13,336 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 0.40 (13336 hom., cov: 32)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	XM_047434582.1	c.1212+13396C>T		intron_variant	Intron 4 of 4		XP_047290538.1
SHISA9	XM_011522642.3	c.1212+13396C>T		intron_variant	Intron 4 of 4		XP_011520944.1
SHISA9	XR_007064905.1	n.1556+13396C>T		intron_variant	Intron 4 of 6
SHISA9	XR_932915.3	n.1556+13396C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262801	ENST00000571619.5	n.420+13396C>T		intron_variant	Intron 3 of 4	3
ENSG00000262801	ENST00000574540.2	n.594+13201C>T		intron_variant	Intron 2 of 3	3
ENSG00000262801	ENST00000653029.1	n.401+13396C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60133 AN: 151846 Hom.: 13326 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.396 AC: 60154 AN: 151964 Hom.: 13336 Cov.: 32 AF XY: 0.397 AC XY: 29456 AN XY: 74282

African (AFR) AF: 0.183 AC: 7571 AN: 41448

American (AMR) AF: 0.464 AC: 7092 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3468

East Asian (EAS) AF: 0.569 AC: 2934 AN: 5156

South Asian (SAS) AF: 0.499 AC: 2401 AN: 4814

European-Finnish (FIN) AF: 0.474 AC: 4992 AN: 10532

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32203 AN: 67950

Other (OTH) AF: 0.413 AC: 870 AN: 2108

Alfa AF: 0.417 Hom.: 19944

Bravo AF: 0.389

Asia WGS AF: 0.522 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.45
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1858992; hg19: chr16-13457674;