chr19-32278213-A-G

Position:

• chr19-32278213-A-G

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 0.808 in 151,978 control chromosomes in the GnomAD database, including 49,845 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 0.81 (49845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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: 0.808 AC: 122640 AN: 151860 Hom.: 49787 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.808 AC: 122760 AN: 151978 Hom.: 49845 Cov.: 32 AF XY: 0.807 AC XY: 59974 AN XY: 74284

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.813

Alfa AF: 0.785 Hom.: 6087

Bravo AF: 0.818

Asia WGS AF: 0.881 AC: 3057 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10403365; hg19: chr19-32769119;