19-20716478-A-G

Variant names:

• chr19-20716478-A-G
• rs7258003

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;