NM_005687.5:c.-113C>G

Variant names:

• chr2-222656186-G-C
• rs2166652
• NM_005687.5:c.-113C>G

Variant summary

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

The NM_005687.5(FARSB):​c.-113C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 712,212 control chromosomes in the GnomAD database, including 244,716 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 0.85 (56406 hom., cov: 36)
  • Exomes 𝑓: 0.81 (188310 hom.)
• Consequence: FARSB NM_005687.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

FARSB (HGNC:17800): (phenylalanyl-tRNA synthetase subunit beta) This gene encodes a highly conserved enzyme that belongs to the aminoacyl-tRNA synthetase class IIc subfamily. This enzyme comprises the regulatory beta subunits that form a tetramer with two catalytic alpha subunits. In the presence of ATP, this tetramer is responsible for attaching L-phenylalanine to the terminal adenosine of the appropriate tRNA. A pseudogene located on chromosome 10 has been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

LOC124907985 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARSB	NM_005687.5	c.-113C>G		upstream_gene_variant		ENST00000281828.8	NP_005678.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARSB	ENST00000281828.8	c.-113C>G		upstream_gene_variant		1	NM_005687.5	ENSP00000281828.6

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129948 AN: 152244 Hom.: 56360 Cov.: 36

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.862

GnomAD4 exome AF: 0.813 AC: 455072 AN: 559850 Hom.: 188310 Cov.: 7 AF XY: 0.813 AC XY: 241402 AN XY: 296974

Gnomad4 AFR exome AF: 0.964

Gnomad4 AMR exome AF: 0.727

Gnomad4 ASJ exome AF: 0.864

Gnomad4 EAS exome AF: 0.406

Gnomad4 SAS exome AF: 0.797

Gnomad4 FIN exome AF: 0.780

Gnomad4 NFE exome AF: 0.848

Gnomad4 OTH exome AF: 0.825

GnomAD4 genome AF: 0.853 AC: 130040 AN: 152362 Hom.: 56406 Cov.: 36 AF XY: 0.844 AC XY: 62909 AN XY: 74502

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.857

Alfa AF: 0.788 Hom.: 2377

Bravo AF: 0.856

Asia WGS AF: 0.642 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.65

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: rs2166652; hg19: chr2-223520905; COSMIC: COSV56052419;