10-89016326-A-G

Position:

• chr10-89016326-A-G

Variant summary

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

The NM_000043.6(FAS):​c.*1876A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 218,146 control chromosomes in the GnomAD database, including 59,312 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 0.73 (40532 hom., cov: 32)
  • Exomes 𝑓: 0.75 (18780 hom.)
• Consequence: FAS NM_000043.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAS	NM_000043.6	c.*1876A>G		3_prime_UTR_variant	9/9	ENST00000652046.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAS	ENST00000652046.1	c.*1876A>G		3_prime_UTR_variant	9/9		NM_000043.6	A2

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110488 AN: 151998 Hom.: 40504 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.746

GnomAD4 exome AF: 0.748 AC: 49383 AN: 66030 Hom.: 18780 Cov.: 0 AF XY: 0.748 AC XY: 22868 AN XY: 30564

Gnomad4 AFR exome AF: 0.679

Gnomad4 AMR exome AF: 0.797

Gnomad4 ASJ exome AF: 0.742

Gnomad4 EAS exome AF: 0.949

Gnomad4 SAS exome AF: 0.814

Gnomad4 FIN exome AF: 0.792

Gnomad4 NFE exome AF: 0.704

Gnomad4 OTH exome AF: 0.737

GnomAD4 genome AF: 0.727 AC: 110573 AN: 152116 Hom.: 40532 Cov.: 32 AF XY: 0.734 AC XY: 54591 AN XY: 74358

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.742

Alfa AF: 0.729 Hom.: 6608

Bravo AF: 0.723

Asia WGS AF: 0.864 AC: 3003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800623; hg19: chr10-90776083;