19-32278213-A-G

Variant names:

• chr19-32278213-A-G
• rs10403365

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;