rs16982345

Variant names:

• chr19-18389912-G-A
• rs16982345

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 0.22 in 152,128 control chromosomes in the GnomAD database, including 3,854 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 0.22 (3854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 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: 0.220 AC: 33494 AN: 152010 Hom.: 3856 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.220 AC: 33494 AN: 152128 Hom.: 3854 Cov.: 32 AF XY: 0.220 AC XY: 16360 AN XY: 74380

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.218

Alfa AF: 0.245 Hom.: 6277

Bravo AF: 0.209

Asia WGS AF: 0.278 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16982345; hg19: chr19-18500722;