19-50851070-A-G

Variant names:

• chr19-50851070-A-G
• rs266864
• ENST00000598079.1:n.373A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000598079.1(ENSG00000267968):​n.373A>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: ENSG00000267968 ENST00000598079.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 4 publications found

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598079.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105372441	NR_131203.1		n.373A>G		non_coding_transcript_exon	Exon 3 of 3
	LOC105372441	NR_131205.1		n.390A>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267968	ENST00000598079.1	TSL:3	n.373A>G		non_coding_transcript_exon	Exon 3 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 5 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.724 AC: 30016 AN: 41460

American (AMR) AF: 0.746 AC: 11382 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2767 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4268 AN: 5160

South Asian (SAS) AF: 0.752 AC: 3628 AN: 4826

European-Finnish (FIN) AF: 0.886 AC: 9395 AN: 10606

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53987 AN: 67974

Other (OTH) AF: 0.773 AC: 1632 AN: 2112

Alfa AF: 0.783 Hom.: 35566

Bravo AF: 0.761

Asia WGS AF: 0.805 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		-0.79

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs266864;

hg19: chr19-51354326;