19-9291028-G-A

Position:

• chr19-9291028-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 0.613 in 151,792 control chromosomes in the GnomAD database, including 29,052 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 0.61 (29052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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 = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93023 AN: 151674 Hom.: 29012 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.613 AC: 93117 AN: 151792 Hom.: 29052 Cov.: 32 AF XY: 0.607 AC XY: 44994 AN XY: 74174

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.630

Alfa AF: 0.600 Hom.: 13831

Bravo AF: 0.629

Asia WGS AF: 0.546 AC: 1882 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7247108; hg19: chr19-9401704;