rs7200108

Variant names:

• chr16-13345027-T-C
• rs7200108
• XM_047434582.1:c.971-5153T>C

Variant summary

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

The ENST00000571619.5(ENSG00000262801):​n.179-5153T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,066 control chromosomes in the GnomAD database, including 3,023 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 0.18 (3023 hom., cov: 32)
• Consequence: ENSG00000262801 ENST00000571619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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.179-5153T>C		intron	N/A
	ENSG00000262801	ENST00000574540.2	TSL:3	n.158-5153T>C		intron	N/A
	ENSG00000262801	ENST00000653029.1		n.160-5153T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27251 AN: 151948 Hom.: 3006 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.180 AC: 27301 AN: 152066 Hom.: 3023 Cov.: 32 AF XY: 0.180 AC XY: 13368 AN XY: 74334

African (AFR) AF: 0.298 AC: 12353 AN: 41486

American (AMR) AF: 0.189 AC: 2878 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3472

East Asian (EAS) AF: 0.189 AC: 978 AN: 5174

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4816

European-Finnish (FIN) AF: 0.112 AC: 1184 AN: 10586

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7637 AN: 67966

Other (OTH) AF: 0.165 AC: 348 AN: 2104

Alfa AF: 0.135 Hom.: 2118

Bravo AF: 0.189

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.50
PhyloP100		-0.43

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: rs7200108;

hg19: chr16-13438884;