19-15898482-A-G

Variant names:

• chr19-15898482-A-G
• rs3093089

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 0.296 in 151,670 control chromosomes in the GnomAD database, including 7,082 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 0.30 (7082 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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: 0.296 AC: 44827 AN: 151552 Hom.: 7087 Cov.: 29

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.296 AC: 44821 AN: 151670 Hom.: 7082 Cov.: 29 AF XY: 0.294 AC XY: 21799 AN XY: 74112

African (AFR) AF: 0.191 AC: 7905 AN: 41342

American (AMR) AF: 0.309 AC: 4710 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.232 AC: 1194 AN: 5144

South Asian (SAS) AF: 0.274 AC: 1315 AN: 4798

European-Finnish (FIN) AF: 0.376 AC: 3944 AN: 10498

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23826 AN: 67858

Other (OTH) AF: 0.276 AC: 583 AN: 2110

Alfa AF: 0.318 Hom.: 10388

Bravo AF: 0.285

Asia WGS AF: 0.235 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.48
PhyloP100		0.35
PromoterAI		0.0084	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3093089; hg19: chr19-16009292;