chr19-33573148-C-T

Variant names:

• chr19-33573148-C-T
• rs3898492

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 0.363 in 151,950 control chromosomes in the GnomAD database, including 10,756 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 0.36 (10756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.363 AC: 55092 AN: 151832 Hom.: 10762 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.363 AC: 55092 AN: 151950 Hom.: 10756 Cov.: 31 AF XY: 0.357 AC XY: 26548 AN XY: 74280

African (AFR) AF: 0.218 AC: 9065 AN: 41496

American (AMR) AF: 0.358 AC: 5467 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2068 AN: 5128

South Asian (SAS) AF: 0.364 AC: 1749 AN: 4810

European-Finnish (FIN) AF: 0.351 AC: 3705 AN: 10548

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30270 AN: 67920

Other (OTH) AF: 0.384 AC: 810 AN: 2110

Alfa AF: 0.419 Hom.: 40541

Bravo AF: 0.359

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.19
DANN	Benign	0.86
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs3898492; hg19: chr19-34064054;