rs78192384

Variant names:

• chr18-3041399-G-A
• rs78192384

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 0.0416 in 152,218 control chromosomes in the GnomAD database, including 258 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 0.042 (258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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: 0.0416 AC: 6334 AN: 152100 Hom.: 259 Cov.: 32

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0416 AC: 6337 AN: 152218 Hom.: 258 Cov.: 32 AF XY: 0.0440 AC XY: 3271 AN XY: 74416

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.0209

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.0334

Gnomad4 FIN AF: 0.0579

Gnomad4 NFE AF: 0.0195

Gnomad4 OTH AF: 0.0427

Alfa AF: 0.0288 Hom.: 26

Bravo AF: 0.0425

Asia WGS AF: 0.110 AC: 380 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	0.26
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78192384; hg19: chr18-3041397;