XM_006717819.4:c.-5771C>A

Variant names:

• chr10-88967577-C-A
• rs1926203
• XM_006717819.4:c.-5771C>A

Variant summary

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

The XM_006717819.4(FAS):​c.-5771C>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,026 control chromosomes in the GnomAD database, including 26,555 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 0.58 (26555 hom., cov: 32)
• Consequence: FAS XM_006717819.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

Genes affected

FAS (HGNC:11920): (Fas cell surface death receptor) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor contains a death domain. It has been shown to play a central role in the physiological regulation of programmed cell death, and has been implicated in the pathogenesis of various malignancies and diseases of the immune system. The interaction of this receptor with its ligand allows the formation of a death-inducing signaling complex that includes Fas-associated death domain protein (FADD), caspase 8, and caspase 10. The autoproteolytic processing of the caspases in the complex triggers a downstream caspase cascade, and leads to apoptosis. This receptor has been also shown to activate NF-kappaB, MAPK3/ERK1, and MAPK8/JNK, and is found to be involved in transducing the proliferating signals in normal diploid fibroblast and T cells. Several alternatively spliced transcript variants have been described, some of which are candidates for nonsense-mediated mRNA decay (NMD). The isoforms lacking the transmembrane domain may negatively regulate the apoptosis mediated by the full length isoform. [provided by RefSeq, Mar 2011]

STAMBPL1 (HGNC:24105): (STAM binding protein like 1) Predicted to enable Lys63-specific deubiquitinase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein K63-linked deubiquitination. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACTA2 (HGNC:130): (actin alpha 2, smooth muscle) This gene encodes one of six different actin proteins. Actins are highly conserved proteins that are involved in cell motility, structure, integrity, and intercellular signaling. The encoded protein is a smooth muscle actin that is involved in vascular contractility and blood pressure homeostasis. Mutations in this gene cause a variety of vascular diseases, such as thoracic aortic disease, coronary artery disease, stroke, and Moyamoya disease, as well as multisystemic smooth muscle dysfunction syndrome. [provided by RefSeq, Sep 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAS	XM_006717819.4	c.-5771C>A		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10		XP_006717882.1
FAS	XM_006717819.4	c.-5771C>A		5_prime_UTR_variant	Exon 1 of 10		XP_006717882.1
ACTA2	NM_001141945.3	c.-23-18624G>T		intron_variant	Intron 1 of 8		NP_001135417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAMBPL1	ENST00000371927.7	c.1255-5605C>A		intron_variant	Intron 10 of 10	2		ENSP00000360995.3
ACTA2	ENST00000415557.2	c.-23-18624G>T		intron_variant	Intron 1 of 8	3		ENSP00000396730.2
ACTA2	ENST00000458159.6	c.-23-18624G>T		intron_variant	Intron 1 of 8	3		ENSP00000398239.2
FAS	ENST00000688239.1	n.95-5605C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87813 AN: 151908 Hom.: 26530 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.578 AC: 87884 AN: 152026 Hom.: 26555 Cov.: 32 AF XY: 0.566 AC XY: 42033 AN XY: 74316

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.555

Alfa AF: 0.634 Hom.: 67835

Bravo AF: 0.571

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1926203; hg19: chr10-90727334;