16-13437655-G-C

Variant names:

• chr16-13437655-G-C
• rs1001937
• XM_047434582.1:c.1213-13307G>C

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.421-36555G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,772 control chromosomes in the GnomAD database, including 17,083 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 0.46 (17083 hom., cov: 30)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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.421-36555G>C		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.595-36555G>C		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.402-36555G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69630 AN: 151654 Hom.: 17050 Cov.: 30

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.459 AC: 69720 AN: 151772 Hom.: 17083 Cov.: 30 AF XY: 0.456 AC XY: 33818 AN XY: 74150

African (AFR) AF: 0.626 AC: 25915 AN: 41378

American (AMR) AF: 0.410 AC: 6248 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1563 AN: 5140

South Asian (SAS) AF: 0.190 AC: 912 AN: 4796

European-Finnish (FIN) AF: 0.453 AC: 4759 AN: 10516

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27352 AN: 67910

Other (OTH) AF: 0.440 AC: 928 AN: 2110

Alfa AF: 0.448 Hom.: 2008

Bravo AF: 0.468

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.095
DANN	Benign	0.36
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1001937; hg19: chr16-13531512;