rs7200108

Variant names:

• chr16-13345027-T-C
• rs7200108
• ENST00000571619.5:n.179-5153T>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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	XM_047434582.1	c.971-5153T>C		intron_variant	Intron 3 of 4		XP_047290538.1
SHISA9	XM_011522642.3	c.971-5153T>C		intron_variant	Intron 3 of 4		XP_011520944.1
SHISA9	XR_007064905.1	n.1315-5153T>C		intron_variant	Intron 3 of 6
SHISA9	XR_932915.3	n.1315-5153T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262801	ENST00000571619.5	n.179-5153T>C		intron_variant	Intron 2 of 4	3
ENSG00000262801	ENST00000574540.2	n.158-5153T>C		intron_variant	Intron 1 of 3	3
ENSG00000262801	ENST00000653029.1	n.160-5153T>C		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs7200108; hg19: chr16-13438884;