19-50851070-A-G

Variant summary

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

The NR_131205.1(LOC105372441):n.390A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,078 control chromosomes in the GnomAD database, including 46,064 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 0.78 (46061 hom., cov: 31)
  • Exomes 𝑓: 0.88 (3 hom.)
• Consequence: LOC105372441 NR_131205.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372441	NR_131205.1	n.390A>G		non_coding_transcript_exon_variant	3/3
LOC105372441	NR_131203.1	n.373A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598079.1	n.373A>G		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118016 AN: 151954 Hom.: 46042 Cov.: 31

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.769

GnomAD4 exome AF: 0.875 AC: 7 AN: 8 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.833

GnomAD4 genome AF: 0.776 AC: 118079 AN: 152070 Hom.: 46061 Cov.: 31 AF XY: 0.778 AC XY: 57850 AN XY: 74360

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.773

Alfa AF: 0.784 Hom.: 17312

Bravo AF: 0.761

Asia WGS AF: 0.805 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266864; hg19: chr19-51354326;