ENST00000571619.5:n.553-35129G>A

Variant names:

• chr16-13527578-G-A
• rs10521095
• ENST00000571619.5:n.553-35129G>A

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.553-35129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,958 control chromosomes in the GnomAD database, including 7,914 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 0.32 (7914 hom., cov: 32)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262801	ENST00000571619.5	TSL:3	n.553-35129G>A		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.727-35129G>A		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.534-24815G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47887 AN: 151840 Hom.: 7898 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.317

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.315 AC: 47933 AN: 151958 Hom.: 7914 Cov.: 32 AF XY: 0.319 AC XY: 23657 AN XY: 74260

African (AFR) AF: 0.385 AC: 15938 AN: 41400

American (AMR) AF: 0.338 AC: 5162 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2727 AN: 5160

South Asian (SAS) AF: 0.370 AC: 1781 AN: 4816

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10562

Middle Eastern (MID) AF: 0.317 AC: 92 AN: 290

European-Non Finnish (NFE) AF: 0.265 AC: 18045 AN: 67974

Other (OTH) AF: 0.318 AC: 671 AN: 2110

Alfa AF: 0.290 Hom.: 4643

Bravo AF: 0.327

Asia WGS AF: 0.419 AC: 1454 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.77
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10521095; hg19: chr16-13621435;