chr19-39053594-G-T

Variant names:

• chr19-39053594-G-T
• rs930100

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 0.288 in 152,040 control chromosomes in the GnomAD database, including 6,616 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 0.29 (6616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43727 AN: 151922 Hom.: 6599 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.288 AC: 43781 AN: 152040 Hom.: 6616 Cov.: 32 AF XY: 0.294 AC XY: 21847 AN XY: 74296

African (AFR) AF: 0.221 AC: 9172 AN: 41502

American (AMR) AF: 0.322 AC: 4911 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1963 AN: 5144

South Asian (SAS) AF: 0.500 AC: 2408 AN: 4818

European-Finnish (FIN) AF: 0.312 AC: 3299 AN: 10584

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19983 AN: 67936

Other (OTH) AF: 0.283 AC: 596 AN: 2106

Alfa AF: 0.305 Hom.: 3942

Bravo AF: 0.280

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs930100; hg19: chr19-39544234;