19-33818627-A-G

Variant names:

• chr19-33818627-A-G
• rs29941

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.696 in 152,104 control chromosomes in the GnomAD database, including 37,873 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 0.70 (37873 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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: 0.696 AC: 105788 AN: 151986 Hom.: 37829 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.696 AC: 105882 AN: 152104 Hom.: 37873 Cov.: 33 AF XY: 0.691 AC XY: 51361 AN XY: 74350

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.679

Alfa AF: 0.669 Hom.: 50636

Bravo AF: 0.700

Asia WGS AF: 0.479 AC: 1665 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs29941; hg19: chr19-34309532;