rs1858992

Variant names:

• chr16-13363817-C-T
• rs1858992
• XM_047434582.1:c.1212+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

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

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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262801	ENST00000571619.5	TSL:3	n.420+13396C>T		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.594+13201C>T		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.401+13396C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1858992;

hg19: chr16-13457674;