19-54288907-C-G

Variant names:

• chr19-54288907-C-G
• rs386000

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 0.76 in 151,540 control chromosomes in the GnomAD database, including 44,793 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 0.76 (44780 hom., cov: 31)
  • Exomes 𝑓: 0.80 (13 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.033).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.808 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

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115131 AN: 151382 Hom.: 44749 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.788

GnomAD4 exome AF: 0.800 AC: 32 AN: 40 Hom.: 13 Cov.: 0 AF XY: 0.800 AC XY: 24 AN XY: 30

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.875

Gnomad4 NFE exome AF: 0.769

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.760 AC: 115213 AN: 151500 Hom.: 44780 Cov.: 31 AF XY: 0.752 AC XY: 55673 AN XY: 74022

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.788

Alfa AF: 0.780 Hom.: 5455

Bravo AF: 0.751

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.033

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386000; hg19: -;