rs4784384

Variant names:

• chr16-54438149-C-T
• rs4784384
• ENST00000720695.1:n.183-28691C>T

Variant summary

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

The ENST00000720695.1(ENSG00000287885):​n.183-28691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,106 control chromosomes in the GnomAD database, including 4,783 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 0.24 (4783 hom., cov: 32)
• Consequence: ENSG00000287885 ENST00000720695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

Genes affected

ENSG00000287885 (HGNC:58975):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720695.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287885	ENST00000720695.1		n.183-28691C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36161 AN: 151988 Hom.: 4783 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.238 AC: 36170 AN: 152106 Hom.: 4783 Cov.: 32 AF XY: 0.238 AC XY: 17703 AN XY: 74326

African (AFR) AF: 0.129 AC: 5369 AN: 41508

American (AMR) AF: 0.206 AC: 3144 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3468

East Asian (EAS) AF: 0.108 AC: 556 AN: 5158

South Asian (SAS) AF: 0.189 AC: 912 AN: 4814

European-Finnish (FIN) AF: 0.310 AC: 3274 AN: 10554

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20745 AN: 67994

Other (OTH) AF: 0.248 AC: 523 AN: 2110

Alfa AF: 0.285 Hom.: 3355

Bravo AF: 0.225

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4784384;

hg19: chr16-54472061;