rs29941

Positions:

• chr19-33818627-A-G
• chr19-33818627-A-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;