19-10025011-A-G

Variant names:

• chr19-10025011-A-G
• rs1673130

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 0.799 in 151,872 control chromosomes in the GnomAD database, including 49,092 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 (49092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 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: 0.798 AC: 121167 AN: 151756 Hom.: 49037 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.799 AC: 121278 AN: 151872 Hom.: 49092 Cov.: 32 AF XY: 0.799 AC XY: 59275 AN XY: 74196

African (AFR) AF: 0.921 AC: 38211 AN: 41492

American (AMR) AF: 0.770 AC: 11760 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2410 AN: 3462

East Asian (EAS) AF: 0.504 AC: 2594 AN: 5148

South Asian (SAS) AF: 0.774 AC: 3739 AN: 4828

European-Finnish (FIN) AF: 0.822 AC: 8610 AN: 10470

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.757 AC: 51423 AN: 67894

Other (OTH) AF: 0.784 AC: 1656 AN: 2112

Alfa AF: 0.762 Hom.: 70006

Bravo AF: 0.796

Asia WGS AF: 0.726 AC: 2526 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.84
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1673130; hg19: chr19-10135687;