rs17447091

Positions:

• chr10-88971512-T-A

Variant summary

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

The NM_001141945.3(ACTA2):​c.-24+19427A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,240 control chromosomes in the GnomAD database, including 1,000 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 0.10 (1000 hom., cov: 32)
• Consequence: ACTA2 NM_001141945.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

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]

FAS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAS	XM_006717819.4	c.-1836T>A		5_prime_UTR_variant	1/10		XP_006717882.1
ACTA2	NM_001141945.3	c.-24+19427A>T		intron_variant			NP_001135417.1
ACTA2	NM_001320855.2	c.-24+19510A>T		intron_variant			NP_001307784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAMBPL1	ENST00000371927.7	c.1255-1670T>A		intron_variant		2		ENSP00000360995.3
ACTA2	ENST00000415557.2	c.-24+19427A>T		intron_variant		3		ENSP00000396730.2
ACTA2	ENST00000458159.6	c.-24+19510A>T		intron_variant		3		ENSP00000398239.2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15363 AN: 152122 Hom.: 999 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.00807

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.101 AC: 15358 AN: 152240 Hom.: 1000 Cov.: 32 AF XY: 0.0991 AC XY: 7374 AN XY: 74424

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.0789

Gnomad4 EAS AF: 0.00829

Gnomad4 SAS AF: 0.0302

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.0978

Alfa AF: 0.115 Hom.: 152

Bravo AF: 0.0948

Asia WGS AF: 0.0250 AC: 88 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17447091; hg19: chr10-90731269;