rs570317

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;