rs29942

Positions:

• chr19-33818372-A-G

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 0.703 in 152,186 control chromosomes in the GnomAD database, including 38,773 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 (38773 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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: 0.703 AC: 106893 AN: 152068 Hom.: 38726 Cov.: 33

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.703 AC: 106993 AN: 152186 Hom.: 38773 Cov.: 33 AF XY: 0.697 AC XY: 51837 AN XY: 74396

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.682

Alfa AF: 0.686 Hom.: 48939

Bravo AF: 0.708

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs29942; hg19: chr19-34309277;