rs4987873

Variant names:

• chr18-63122764-T-A
• rs4987873
• ENST00000763645.1:n.516-5255T>A

Variant summary

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

The ENST00000763645.1(ENSG00000299452):​n.516-5255T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,136 control chromosomes in the GnomAD database, including 2,081 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 0.15 (2081 hom., cov: 32)
• Consequence: ENSG00000299452 ENST00000763645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 4 publications found

Genes affected

ENSG00000299452 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763645.1. 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
	ENSG00000299452	ENST00000763645.1		n.516-5255T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22169 AN: 152018 Hom.: 2071 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.146 AC: 22199 AN: 152136 Hom.: 2081 Cov.: 32 AF XY: 0.140 AC XY: 10424 AN XY: 74386

African (AFR) AF: 0.275 AC: 11405 AN: 41448

American (AMR) AF: 0.104 AC: 1592 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0594 AC: 287 AN: 4834

European-Finnish (FIN) AF: 0.0901 AC: 954 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6993 AN: 67994

Other (OTH) AF: 0.156 AC: 330 AN: 2114

Alfa AF: 0.125 Hom.: 188

Bravo AF: 0.155

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.96
DANN	Benign	0.41
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs4987873; hg19: chr18-60789997;