rs368794

Variant names:

• chr19-33829547-T-A
• rs368794

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 0.644 in 152,082 control chromosomes in the GnomAD database, including 31,870 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 0.64 (31870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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: 0.644 AC: 97933 AN: 151964 Hom.: 31854 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.644 AC: 97995 AN: 152082 Hom.: 31870 Cov.: 32 AF XY: 0.642 AC XY: 47707 AN XY: 74338

African (AFR) AF: 0.642 AC: 26635 AN: 41488

American (AMR) AF: 0.652 AC: 9957 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1708 AN: 5176

South Asian (SAS) AF: 0.580 AC: 2792 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 7006 AN: 10574

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45736 AN: 67976

Other (OTH) AF: 0.626 AC: 1319 AN: 2108

Alfa AF: 0.664 Hom.: 4151

Bravo AF: 0.644

Asia WGS AF: 0.484 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.28
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs368794; hg19: chr19-34320452;