rs4645878

chr19-48954681-A-G

Variant summary

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

The variant allele was found at a frequency of 0.896 in 383,248 control chromosomes in the GnomAD database, including 154,054 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 0.89 (60916 hom., cov: 34)
  • Exomes 𝑓: 0.90 (93138 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.894 AC: 136017 AN: 152162 Hom.: 60868 Cov.: 34

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.877

GnomAD4 exome AF: 0.898 AC: 207346 AN: 230968 Hom.: 93138 AF XY: 0.898 AC XY: 105510 AN XY: 117538

Gnomad4 AFR exome AF: 0.915

Gnomad4 AMR exome AF: 0.842

Gnomad4 ASJ exome AF: 0.919

Gnomad4 EAS exome AF: 0.967

Gnomad4 SAS exome AF: 0.955

Gnomad4 FIN exome AF: 0.925

Gnomad4 NFE exome AF: 0.884

Gnomad4 OTH exome AF: 0.891

GnomAD4 genome AF: 0.894 AC: 136124 AN: 152280 Hom.: 60916 Cov.: 34 AF XY: 0.896 AC XY: 66725 AN XY: 74466

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.877

Alfa AF: 0.883 Hom.: 56878

Bravo AF: 0.887

Asia WGS AF: 0.915 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.5
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4645878; hg19: chr19-49457938;