19-48946586-G-C

Variant names:

• chr19-48946586-G-C
• rs4802527

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 0.837 in 152,124 control chromosomes in the GnomAD database, including 53,273 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 0.84 (53273 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767

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 (EAS) allele frequency at 95% confidence interval = 0.906 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: 0.837 AC: 127163 AN: 152006 Hom.: 53218 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.837 AC: 127277 AN: 152124 Hom.: 53273 Cov.: 31 AF XY: 0.838 AC XY: 62309 AN XY: 74366

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.826

Alfa AF: 0.818 Hom.: 2544

Bravo AF: 0.831

Asia WGS AF: 0.858 AC: 2986 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	0.77
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4802527; hg19: chr19-49449843;