chr19-48783974-A-G

Variant names:

• chr19-48783974-A-G
• rs570317

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 0.795 in 151,254 control chromosomes in the GnomAD database, including 48,059 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 0.80 (48059 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120159 AN: 151138 Hom.: 47992 Cov.: 30

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.795 AC: 120281 AN: 151254 Hom.: 48059 Cov.: 30 AF XY: 0.794 AC XY: 58630 AN XY: 73860

African (AFR) AF: 0.843 AC: 34807 AN: 41302

American (AMR) AF: 0.811 AC: 12324 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2666 AN: 3438

East Asian (EAS) AF: 0.521 AC: 2661 AN: 5112

South Asian (SAS) AF: 0.695 AC: 3342 AN: 4812

European-Finnish (FIN) AF: 0.820 AC: 8599 AN: 10492

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.788 AC: 53279 AN: 67598

Other (OTH) AF: 0.796 AC: 1671 AN: 2100

Alfa AF: 0.884 Hom.: 12739

Bravo AF: 0.797

Asia WGS AF: 0.645 AC: 2239 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.11
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs570317; hg19: chr19-49287231;