19-20716478-A-G

Position:

• chr19-20716478-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 0.481 in 152,096 control chromosomes in the GnomAD database, including 17,904 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 0.48 (17904 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73149 AN: 151978 Hom.: 17885 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.481 AC: 73202 AN: 152096 Hom.: 17904 Cov.: 33 AF XY: 0.478 AC XY: 35518 AN XY: 74364

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.486

Alfa AF: 0.501 Hom.: 4876

Bravo AF: 0.479

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.0
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7258003; hg19: chr19-20899284;