rs734071

chr3-48478412-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHISA5	NM_016479.6	c.314+765G>T		intron_variant		ENST00000296444.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHISA5	ENST00000296444.7	c.314+765G>T		intron_variant		1	NM_016479.6	P1

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

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.601

Alfa AF: 0.591 Hom.: 6337

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734071; hg19: chr3-48519821;