rs3764563

Positions:

• chr19-15613392-A-G
• chr19-15613392-A-T

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/exons	MANE	Protein	UniProt
		n.15613392A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266951	ENST00000589196.2	n.457T>C		non_coding_transcript_exon_variant	2/2	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;