chr19-18389912-G-A

Position:

• chr19-18389912-G-A

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/exons	MANE	UniProt

Ensembl

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