chr19-48946586-G-C

Variant names:

• chr19-48946586-G-C
• rs4802527

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.822 AC: 34122 AN: 41492

American (AMR) AF: 0.821 AC: 12539 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4807 AN: 5178

South Asian (SAS) AF: 0.834 AC: 4025 AN: 4828

European-Finnish (FIN) AF: 0.875 AC: 9276 AN: 10600

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57090 AN: 67964

Other (OTH) AF: 0.826 AC: 1748 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.52
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs4802527; hg19: chr19-49449843;