rs1516489

Variant names:

• chr3-191804063-A-C
• rs1516489
• ENST00000820043.1:n.100+4395T>G

Variant summary

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

The ENST00000820043.1(ENSG00000306673):​n.100+4395T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 152,250 control chromosomes in the GnomAD database, including 751 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 0.087 (751 hom., cov: 33)
• Consequence: ENSG00000306673 ENST00000820043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

Genes affected

ENSG00000306673 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820043.1. 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
	ENSG00000306673	ENST00000820043.1		n.100+4395T>G		intron	N/A
	ENSG00000306673	ENST00000820044.1		n.254-4596T>G		intron	N/A
	ENSG00000306673	ENST00000820045.1		n.134+4395T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13313 AN: 152132 Hom.: 751 Cov.: 33

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.0875 AC: 13320 AN: 152250 Hom.: 751 Cov.: 33 AF XY: 0.0906 AC XY: 6741 AN XY: 74436

African (AFR) AF: 0.0244 AC: 1014 AN: 41556

American (AMR) AF: 0.135 AC: 2062 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0744 AC: 359 AN: 4824

European-Finnish (FIN) AF: 0.178 AC: 1888 AN: 10596

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7399 AN: 68016

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0978 Hom.: 1660

Bravo AF: 0.0819

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.3
DANN	Benign	0.97
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1516489; hg19: chr3-191521852;