19-29038019-A-G

Variant names:

• chr19-29038019-A-G
• rs8104146

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 0.668 in 152,104 control chromosomes in the GnomAD database, including 35,628 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 0.67 (35628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.668 AC: 101571 AN: 151986 Hom.: 35585 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.668 AC: 101673 AN: 152104 Hom.: 35628 Cov.: 32 AF XY: 0.672 AC XY: 49946 AN XY: 74346

African (AFR) AF: 0.886 AC: 36797 AN: 41528

American (AMR) AF: 0.633 AC: 9664 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3470

East Asian (EAS) AF: 0.768 AC: 3964 AN: 5162

South Asian (SAS) AF: 0.671 AC: 3232 AN: 4814

European-Finnish (FIN) AF: 0.619 AC: 6536 AN: 10564

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37501 AN: 67972

Other (OTH) AF: 0.612 AC: 1293 AN: 2112

Alfa AF: 0.649 Hom.: 6450

Bravo AF: 0.678

Asia WGS AF: 0.759 AC: 2641 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	0.81
DANN	Benign	0.53
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs8104146; hg19: chr19-29528926;