rs4309483

Positions:

• chr18-58418685-A-C
• chr18-58418685-A-T

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 0.698 in 151,976 control chromosomes in the GnomAD database, including 37,786 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 0.70 (37786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.699 AC: 106090 AN: 151858 Hom.: 37770 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.698 AC: 106147 AN: 151976 Hom.: 37786 Cov.: 31 AF XY: 0.697 AC XY: 51783 AN XY: 74280

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.703

Alfa AF: 0.745 Hom.: 69633

Bravo AF: 0.696

Asia WGS AF: 0.721 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4309483; hg19: chr18-56085917;