19-29603679-G-T

Variant names:

• chr19-29603679-G-T
• rs997554

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;