19-55989684-A-G

Variant names:

• chr19-55989684-A-G
• rs306450

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 0.417 in 152,012 control chromosomes in the GnomAD database, including 13,468 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 0.42 (13468 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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 = 0.524 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: 0.417 AC: 63284 AN: 151892 Hom.: 13461 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.424

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.417 AC: 63340 AN: 152012 Hom.: 13468 Cov.: 33 AF XY: 0.410 AC XY: 30441 AN XY: 74308

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.426

Alfa AF: 0.412 Hom.: 20733

Bravo AF: 0.430

Asia WGS AF: 0.488 AC: 1694 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	0.25
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs306450; hg19: chr19-56501050;