19-28772783-G-T

Variant names:

• chr19-28772783-G-T
• rs12462886

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 0.508 in 151,908 control chromosomes in the GnomAD database, including 21,117 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 0.51 (21117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 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: 0.509 AC: 77188 AN: 151788 Hom.: 21118 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.508 AC: 77187 AN: 151908 Hom.: 21117 Cov.: 32 AF XY: 0.503 AC XY: 37328 AN XY: 74248

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.556

Alfa AF: 0.456 Hom.: 2141

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12462886; hg19: chr19-29263690;