19-33830353-G-T

Variant names:

• chr19-33830353-G-T
• rs398426

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 0.23 in 151,942 control chromosomes in the GnomAD database, including 4,628 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 0.23 (4628 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.349 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: 0.230 AC: 34925 AN: 151824 Hom.: 4628 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.230 AC: 34922 AN: 151942 Hom.: 4628 Cov.: 31 AF XY: 0.235 AC XY: 17466 AN XY: 74250

African (AFR) AF: 0.101 AC: 4186 AN: 41462

American (AMR) AF: 0.357 AC: 5443 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3462

East Asian (EAS) AF: 0.147 AC: 761 AN: 5164

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4810

European-Finnish (FIN) AF: 0.324 AC: 3419 AN: 10540

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18236 AN: 67948

Other (OTH) AF: 0.232 AC: 489 AN: 2110

Alfa AF: 0.254 Hom.: 11270

Bravo AF: 0.229

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.2
DANN	Benign	0.92
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs398426; hg19: chr19-34321258;