chr14-50656877-C-T

Position:

• chr14-50656877-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021818.4(SAV1):​c.535+8302G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,946 control chromosomes in the GnomAD database, including 18,289 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 0.48 (18289 hom., cov: 31)
• Consequence: SAV1 NM_021818.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

SAV1 (HGNC:17795): (salvador family WW domain containing protein 1) WW domain-containing proteins are found in all eukaryotes and play an important role in the regulation of a wide variety of cellular functions such as protein degradation, transcription, and RNA splicing. This gene encodes a protein with two WW domains, a SARAH domain, and a coiled-coil region and is ubiquitously expressed in adult tissues. This protein binds to MST1 (mammalian sterile 20-like kinase 1) and promotes MST1-induced apoptosis. It has also been shown to bind to HAX1 (hematopoietic cell-specific protein 1 (HS1)-associated protein X-1) and to attenuate the anti-apoptotic effects of HAX1. Studies in human and mouse suggest this gene acts as a tumor suppressor. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAV1	NM_021818.4	c.535+8302G>A		intron_variant		ENST00000324679.5	NP_068590.1
SAV1	XM_011537057.4	c.436+8302G>A		intron_variant			XP_011535359.1
SAV1	XM_047431659.1	c.536-7488G>A		intron_variant			XP_047287615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAV1	ENST00000324679.5	c.535+8302G>A		intron_variant		1	NM_021818.4	ENSP00000324729.4
SAV1	ENST00000555720.5	c.331+8302G>A		intron_variant		1		ENSP00000451492.1
SAV1	ENST00000553731.1	c.187+8302G>A		intron_variant		5		ENSP00000450571.1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72486 AN: 151828 Hom.: 18274 Cov.: 31

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.477 AC: 72527 AN: 151946 Hom.: 18289 Cov.: 31 AF XY: 0.482 AC XY: 35819 AN XY: 74244

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.473

Alfa AF: 0.501 Hom.: 19537

Bravo AF: 0.476

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs923908; hg19: chr14-51123595;