rs734071

Variant names:

• chr3-48478412-C-A
• rs734071
• NM_016479.6:c.314+765G>T

Variant summary

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

The NM_016479.6(SHISA5):​c.314+765G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,902 control chromosomes in the GnomAD database, including 27,851 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 0.61 (27851 hom., cov: 32)
• Consequence: SHISA5 NM_016479.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 7 publications found

Genes affected

SHISA5 (HGNC:30376): (shisa family member 5) This gene encodes a member of the shisa family. The encoded protein is localized to the endoplasmic reticulum, and together with p53 induces apoptosis in a caspase-dependent manner. Alternative splicing results in multiple transcript variants. Related pseudogenes of this gene are found on chromosome X. [provided by RefSeq, Apr 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016479.6. 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
	SHISA5	NM_016479.6	MANE Select	c.314+765G>T		intron	N/A	NP_057563.3
	SHISA5	NM_001272065.3		c.293+765G>T		intron	N/A	NP_001258994.1
	SHISA5	NM_001272066.2		c.221+765G>T		intron	N/A	NP_001258995.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHISA5	ENST00000296444.7	TSL:1 MANE Select	c.314+765G>T		intron	N/A	ENSP00000296444.2
	SHISA5	ENST00000443308.6	TSL:2	c.293+765G>T		intron	N/A	ENSP00000395373.2
	SHISA5	ENST00000442747.5	TSL:2	c.221+765G>T		intron	N/A	ENSP00000408223.1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91828 AN: 151784 Hom.: 27827 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.605 AC: 91902 AN: 151902 Hom.: 27851 Cov.: 32 AF XY: 0.610 AC XY: 45307 AN XY: 74216

African (AFR) AF: 0.594 AC: 24613 AN: 41424

American (AMR) AF: 0.672 AC: 10256 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3470

East Asian (EAS) AF: 0.687 AC: 3536 AN: 5150

South Asian (SAS) AF: 0.722 AC: 3474 AN: 4810

European-Finnish (FIN) AF: 0.625 AC: 6593 AN: 10546

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39389 AN: 67930

Other (OTH) AF: 0.601 AC: 1267 AN: 2108

Alfa AF: 0.590 Hom.: 10156

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs734071; hg19: chr3-48519821;