rs2043599

chr19-55939683-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 0.0613 in 152,232 control chromosomes in the GnomAD database, including 334 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 0.061 (334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 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: 0.0612 AC: 9315 AN: 152114 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0613 AC: 9330 AN: 152232 Hom.: 334 Cov.: 32 AF XY: 0.0634 AC XY: 4719 AN XY: 74434

Gnomad4 AFR AF: 0.0467

Gnomad4 AMR AF: 0.0949

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.0653

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0344

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0677

Alfa AF: 0.0632 Hom.: 681

Bravo AF: 0.0623

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.5
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2043599; hg19: chr19-56451049;