chr19-402556-C-G

Position:

• chr19-402556-C-G

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 0.58 in 152,220 control chromosomes in the GnomAD database, including 27,857 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 0.58 (27857 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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 (AFR) allele frequency at 95% confidence interval = 0.826 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: 0.580 AC: 88149 AN: 152100 Hom.: 27810 Cov.: 35

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.580 AC: 88252 AN: 152220 Hom.: 27857 Cov.: 35 AF XY: 0.584 AC XY: 43462 AN XY: 74408

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.532

Alfa AF: 0.516 Hom.: 2700

Bravo AF: 0.595

Asia WGS AF: 0.606 AC: 2104 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	0.59
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2012035; hg19: chr19-402556;