19-28772783-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;