19-28772783-G-T

Variant names:

• chr19-28772783-G-T
• rs12462886

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.326 AC: 13506 AN: 41408

American (AMR) AF: 0.565 AC: 8630 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2146 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1479 AN: 5158

South Asian (SAS) AF: 0.587 AC: 2829 AN: 4816

European-Finnish (FIN) AF: 0.449 AC: 4730 AN: 10546

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41926 AN: 67930

Other (OTH) AF: 0.556 AC: 1174 AN: 2112

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs12462886; hg19: chr19-29263690;