19-2059586-T-C

Variant names:

• chr19-2059586-T-C
• rs10404242

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 0.401 in 152,158 control chromosomes in the GnomAD database, including 14,000 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 0.40 (14000 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 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: 0.401 AC: 60963 AN: 152038 Hom.: 13951 Cov.: 34

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.401 AC: 61081 AN: 152158 Hom.: 14000 Cov.: 34 AF XY: 0.395 AC XY: 29354 AN XY: 74390

African (AFR) AF: 0.628 AC: 26095 AN: 41536

American (AMR) AF: 0.365 AC: 5575 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3466

East Asian (EAS) AF: 0.256 AC: 1323 AN: 5158

South Asian (SAS) AF: 0.378 AC: 1822 AN: 4824

European-Finnish (FIN) AF: 0.239 AC: 2534 AN: 10608

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21272 AN: 67956

Other (OTH) AF: 0.411 AC: 867 AN: 2112

Alfa AF: 0.327 Hom.: 15314

Bravo AF: 0.422

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.62
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10404242; hg19: chr19-2059585;