19-34889600-G-A

Position:

• chr19-34889600-G-A

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 0.0593 in 152,134 control chromosomes in the GnomAD database, including 697 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 0.059 (697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.0593 AC: 9016 AN: 152016 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00943

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00919

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0593 AC: 9018 AN: 152134 Hom.: 697 Cov.: 32 AF XY: 0.0586 AC XY: 4356 AN XY: 74368

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0223

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.00926

Gnomad4 SAS AF: 0.0987

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00919

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0164 Hom.: 176

Bravo AF: 0.0645

Asia WGS AF: 0.0560 AC: 194 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	7.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2651090; hg19: chr19-35380504;