chr19-33843009-C-T

Variant names:

• chr19-33843009-C-T
• rs166988

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 0.726 in 151,950 control chromosomes in the GnomAD database, including 41,277 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 0.73 (41277 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 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: 0.726 AC: 110222 AN: 151832 Hom.: 41241 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.726 AC: 110305 AN: 151950 Hom.: 41277 Cov.: 31 AF XY: 0.717 AC XY: 53230 AN XY: 74282

African (AFR) AF: 0.823 AC: 34153 AN: 41484

American (AMR) AF: 0.645 AC: 9850 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3468

East Asian (EAS) AF: 0.144 AC: 739 AN: 5136

South Asian (SAS) AF: 0.501 AC: 2410 AN: 4806

European-Finnish (FIN) AF: 0.733 AC: 7726 AN: 10546

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50754 AN: 67938

Other (OTH) AF: 0.704 AC: 1485 AN: 2110

Alfa AF: 0.729 Hom.: 173048

Bravo AF: 0.726

Asia WGS AF: 0.326 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs166988; hg19: chr19-34333914;