18-58418685-A-C

Variant names:

• chr18-58418685-A-C
• rs4309483
• ENST00000768486.1:n.684T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000768486.1(ENSG00000300063):​n.684T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000300063 ENST00000768486.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 14 publications found

Genes affected

ENSG00000300063 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768486.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000300063	ENST00000768486.1		n.684T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000300063	ENST00000768487.1		n.297T>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000300063	ENST00000768490.1		n.504T>G		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.552 AC: 22863 AN: 41418

American (AMR) AF: 0.771 AC: 11781 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2417 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4278 AN: 5166

South Asian (SAS) AF: 0.643 AC: 3091 AN: 4810

European-Finnish (FIN) AF: 0.742 AC: 7843 AN: 10566

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51464 AN: 67958

Other (OTH) AF: 0.703 AC: 1481 AN: 2108

Alfa AF: 0.739 Hom.: 159968

Bravo AF: 0.696

Asia WGS AF: 0.721 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs4309483; hg19: chr18-56085917;