rs4862379

Variant names:

• chr4-184553404-G-A
• rs4862379
• ENST00000846822.1:n.184-957G>A

Variant summary

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

The ENST00000846822.1(ENSG00000310055):​n.184-957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0732 in 152,186 control chromosomes in the GnomAD database, including 453 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 0.073 (453 hom., cov: 32)
• Consequence: ENSG00000310055 ENST00000846822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 2 publications found

Genes affected

ENSG00000310055 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846822.1. 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
	ENSG00000310055	ENST00000846822.1		n.184-957G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0733 AC: 11144 AN: 152068 Hom.: 452 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.0732 AC: 11147 AN: 152186 Hom.: 453 Cov.: 32 AF XY: 0.0734 AC XY: 5465 AN XY: 74420

African (AFR) AF: 0.0743 AC: 3083 AN: 41478

American (AMR) AF: 0.0699 AC: 1068 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3470

East Asian (EAS) AF: 0.0555 AC: 288 AN: 5190

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4824

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10616

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5122 AN: 68006

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.0806 Hom.: 571

Bravo AF: 0.0765

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.93
PhyloP100		-0.099

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: rs4862379;

hg19: chr4-185474558;