rs570317

Variant names:

• chr19-48783974-A-G
• rs570317

Your query was ambiguous. Multiple possible variants found:

• chr19-48783974-A-G
• chr19-48783974-A-T

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 0.795 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.795 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

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.796

Alfa AF: 0.802 Hom.: 6092

Bravo AF: 0.797

Asia WGS AF: 0.645 AC: 2239 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs570317; hg19: chr19-49287231;