rs29942

Variant names:

• chr19-33818372-A-G
• rs29942

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 0.703 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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.846 AC: 35142 AN: 41536

American (AMR) AF: 0.651 AC: 9950 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2574 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5184

South Asian (SAS) AF: 0.613 AC: 2960 AN: 4828

European-Finnish (FIN) AF: 0.610 AC: 6445 AN: 10572

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46451 AN: 67998

Other (OTH) AF: 0.682 AC: 1438 AN: 2110

Alfa AF: 0.690 Hom.: 62634

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs29942; hg19: chr19-34309277;