19-15613392-A-G

Variant names:

• chr19-15613392-A-G
• rs3764563
• ENST00000589196.2:n.457T>C

Variant summary

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

The ENST00000589196.2(ENSG00000266951):​n.457T>C 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 0.915 in 152,294 control chromosomes in the GnomAD database, including 63,776 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 0.91 (63762 hom., cov: 32)
  • Exomes 𝑓: 0.94 (14 hom.)
• Consequence: ENSG00000266951 ENST00000589196.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

ENSG00000266951 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266951	ENST00000589196.2	n.457T>C		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139200 AN: 152144 Hom.: 63714 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.919

GnomAD4 exome AF: 0.938 AC: 30 AN: 32 Hom.: 14 Cov.: 0 AF XY: 0.962 AC XY: 25 AN XY: 26

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.909

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.915 AC: 139306 AN: 152262 Hom.: 63762 Cov.: 32 AF XY: 0.915 AC XY: 68116 AN XY: 74444

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.915

Alfa AF: 0.905 Hom.: 81420

Bravo AF: 0.921

Asia WGS AF: 0.875 AC: 3044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3764563; hg19: chr19-15724203;