rs8048671

Variant names:

• chr16-13242587-C-G
• rs8048671
• XM_047434582.1:c.970+39038C>G

Variant summary

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

The XM_047434582.1(SHISA9):​c.970+39038C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,156 control chromosomes in the GnomAD database, including 5,112 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 0.25 (5112 hom., cov: 32)
• Consequence: SHISA9 XM_047434582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA9	XM_047434582.1	c.970+39038C>G		intron_variant	Intron 3 of 4		XP_047290538.1
SHISA9	XM_011522642.3	c.970+39038C>G		intron_variant	Intron 3 of 4		XP_011520944.1
SHISA9	XR_007064905.1	n.1314+39038C>G		intron_variant	Intron 3 of 6
SHISA9	XR_932915.3	n.1314+39038C>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38518 AN: 152038 Hom.: 5101 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.253 AC: 38558 AN: 152156 Hom.: 5112 Cov.: 32 AF XY: 0.251 AC XY: 18637 AN XY: 74384

African (AFR) AF: 0.311 AC: 12926 AN: 41498

American (AMR) AF: 0.193 AC: 2945 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3472

East Asian (EAS) AF: 0.391 AC: 2015 AN: 5154

South Asian (SAS) AF: 0.200 AC: 963 AN: 4826

European-Finnish (FIN) AF: 0.160 AC: 1693 AN: 10588

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16152 AN: 68010

Other (OTH) AF: 0.271 AC: 573 AN: 2114

Alfa AF: 0.237 Hom.: 566

Bravo AF: 0.260

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.43
DANN	Benign	0.62
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs8048671; hg19: chr16-13336444;