19-29603679-G-T

Position:

• chr19-29603679-G-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 0.835 in 152,166 control chromosomes in the GnomAD database, including 53,037 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 0.83 (53037 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

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 (SAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126944 AN: 152048 Hom.: 53000 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.835 AC: 127031 AN: 152166 Hom.: 53037 Cov.: 32 AF XY: 0.837 AC XY: 62237 AN XY: 74388

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.855

Alfa AF: 0.842 Hom.: 29289

Bravo AF: 0.834

Asia WGS AF: 0.863 AC: 3002 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	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997554; hg19: chr19-30094586;