chr19-402556-C-G

Variant names:

• chr19-402556-C-G
• rs2012035

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 0.58 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.833 AC: 34645 AN: 41570

American (AMR) AF: 0.589 AC: 9011 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3687 AN: 5172

South Asian (SAS) AF: 0.532 AC: 2568 AN: 4826

European-Finnish (FIN) AF: 0.508 AC: 5384 AN: 10598

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29874 AN: 67978

Other (OTH) AF: 0.532 AC: 1123 AN: 2112

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2012035; hg19: chr19-402556;