18-3041399-G-A

Position:

• chr18-3041399-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 0.0416 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;