19-47213090-T-A

Position:

• chr19-47213090-T-A

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 0.784 in 152,016 control chromosomes in the GnomAD database, including 47,399 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 0.78 (47399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 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: 0.783 AC: 119002 AN: 151900 Hom.: 47348 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.784 AC: 119111 AN: 152016 Hom.: 47399 Cov.: 32 AF XY: 0.786 AC XY: 58408 AN XY: 74296

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.779

Alfa AF: 0.748 Hom.: 5355

Bravo AF: 0.789

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884171; hg19: chr19-47716347;