rs2967890

Positions:

• chr19-12929833-G-A
• chr19-12929833-G-C

Variant summary

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

The NM_004461.3(FARSA):​c.503+390C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,110 control chromosomes in the GnomAD database, including 51,567 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 0.82 (51567 hom., cov: 31)
• Consequence: FARSA NM_004461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

Genes affected

FARSA (HGNC:3592): (phenylalanyl-tRNA synthetase subunit alpha) Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. This gene encodes a product which is similar to the catalytic subunit of prokaryotic and Saccharomyces cerevisiae phenylalanyl-tRNA synthetases (PheRS). This gene product has been shown to be expressed in a tumor-selective and cell cycle stage- and differentiation-dependent manner, the first member of the tRNA synthetase gene family shown to exhibit this type of regulated expression [provided by RefSeq, Jul 2008]

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 = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FARSA	NM_004461.3	c.503+390C>T		intron_variant		ENST00000314606.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FARSA	ENST00000314606.9	c.503+390C>T		intron_variant		1	NM_004461.3	P1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124661 AN: 151992 Hom.: 51520 Cov.: 31

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.820 AC: 124756 AN: 152110 Hom.: 51567 Cov.: 31 AF XY: 0.823 AC XY: 61174 AN XY: 74348

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.784

Alfa AF: 0.779 Hom.: 59440

Bravo AF: 0.817

Asia WGS AF: 0.854 AC: 2971 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	0.81
DANN	Benign	0.38

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: rs2967890; hg19: chr19-13040647;