chr19-20429839-T-C

Variant names:

• chr19-20429839-T-C
• rs6511105

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 0.066 in 149,884 control chromosomes in the GnomAD database, including 1,441 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 0.066 (1441 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 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: 0.0660 AC: 9882 AN: 149770 Hom.: 1436 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00858

Gnomad SAS AF: 0.00519

Gnomad FIN AF: 0.00362

Gnomad MID AF: 0.0367

Gnomad NFE AF: 0.00731

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0660 AC: 9896 AN: 149884 Hom.: 1441 Cov.: 31 AF XY: 0.0637 AC XY: 4661 AN XY: 73156

African (AFR) AF: 0.214 AC: 8665 AN: 40518

American (AMR) AF: 0.0310 AC: 466 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 51 AN: 3390

East Asian (EAS) AF: 0.00861 AC: 43 AN: 4996

South Asian (SAS) AF: 0.00498 AC: 23 AN: 4620

European-Finnish (FIN) AF: 0.00362 AC: 38 AN: 10506

Middle Eastern (MID) AF: 0.0396 AC: 11 AN: 278

European-Non Finnish (NFE) AF: 0.00731 AC: 494 AN: 67586

Other (OTH) AF: 0.0511 AC: 105 AN: 2056

Alfa AF: 0.0417 Hom.: 163

Asia WGS AF: 0.0180 AC: 64 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.46
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs6511105; hg19: chr19-20612645;