rs4833233

Variant names:

• chr4-121767589-G-A
• rs4833233
• ENST00000746424.1:n.241-767G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-121767589-G-A
• chr4-121767589-G-C
• chr4-121767589-G-T

Variant summary

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

The ENST00000746424.1(PP12613):​n.241-767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,770 control chromosomes in the GnomAD database, including 20,377 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 0.52 (20377 hom., cov: 30)
• Consequence: PP12613 ENST00000746424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503
• Publications: 12 publications found

Genes affected

PP12613 (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 (SAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746424.1. 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
	PP12613	ENST00000746424.1		n.241-767G>A		intron	N/A
	PP12613	ENST00000746425.1		n.239-773G>A		intron	N/A
	PP12613	ENST00000746426.1		n.235-183G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78193 AN: 151652 Hom.: 20361 Cov.: 30

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.516 AC: 78262 AN: 151770 Hom.: 20377 Cov.: 30 AF XY: 0.515 AC XY: 38153 AN XY: 74152

African (AFR) AF: 0.558 AC: 23055 AN: 41346

American (AMR) AF: 0.550 AC: 8402 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1837 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2215 AN: 5156

South Asian (SAS) AF: 0.562 AC: 2688 AN: 4784

European-Finnish (FIN) AF: 0.451 AC: 4733 AN: 10490

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33664 AN: 67938

Other (OTH) AF: 0.511 AC: 1078 AN: 2110

Alfa AF: 0.508 Hom.: 62948

Bravo AF: 0.524

Asia WGS AF: 0.515 AC: 1792 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	13
DANN	Benign	0.63
PhyloP100		0.50

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: rs4833233;

hg19: chr4-122688744;