ENST00000768485.1:n.103+5038G>T

Variant names:

• chr18-58442627-C-A
• rs8099014
• ENST00000768485.1:n.103+5038G>T

Variant summary

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

The ENST00000768485.1(ENSG00000300063):​n.103+5038G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,094 control chromosomes in the GnomAD database, including 33,697 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 0.65 (33697 hom., cov: 33)
• Consequence: ENSG00000300063 ENST00000768485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 11 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768485.1. 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	ENST00000768485.1		n.103+5038G>T		intron	N/A
	ENSG00000300063	ENST00000768486.1		n.183+5038G>T		intron	N/A
	ENSG00000300063	ENST00000768487.1		n.85+5038G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99242 AN: 151976 Hom.: 33691 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.653 AC: 99271 AN: 152094 Hom.: 33697 Cov.: 33 AF XY: 0.652 AC XY: 48526 AN XY: 74372

African (AFR) AF: 0.446 AC: 18485 AN: 41464

American (AMR) AF: 0.730 AC: 11154 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2521 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3904 AN: 5184

South Asian (SAS) AF: 0.626 AC: 3023 AN: 4828

European-Finnish (FIN) AF: 0.724 AC: 7647 AN: 10566

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.739 AC: 50204 AN: 67980

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.709 Hom.: 136583

Bravo AF: 0.647

Asia WGS AF: 0.674 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs8099014; hg19: chr18-56109859;