chr19-55939683-A-G

Variant names:

• chr19-55939683-A-G
• rs2043599

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0467 AC: 1940 AN: 41534

American (AMR) AF: 0.0949 AC: 1450 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3470

East Asian (EAS) AF: 0.0653 AC: 339 AN: 5190

South Asian (SAS) AF: 0.169 AC: 812 AN: 4812

European-Finnish (FIN) AF: 0.0344 AC: 365 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4064 AN: 68024

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.0631 Hom.: 1097

Bravo AF: 0.0623

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.61
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs2043599; hg19: chr19-56451049;