18-3041399-G-A

Variant names:

• chr18-3041399-G-A
• rs78192384

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 0.0416 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
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0608 AC: 2525 AN: 41540

American (AMR) AF: 0.0209 AC: 320 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1143 AN: 5172

South Asian (SAS) AF: 0.0334 AC: 161 AN: 4824

European-Finnish (FIN) AF: 0.0579 AC: 613 AN: 10588

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0195 AC: 1328 AN: 68020

Other (OTH) AF: 0.0427 AC: 90 AN: 2110

Alfa AF: 0.0363 Hom.: 99

Bravo AF: 0.0425

Asia WGS AF: 0.110 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.62
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs78192384; hg19: chr18-3041397; COSMIC: COSV107178804;