4-12933821-C-G

Variant names:

• chr4-12933821-C-G
• rs224001
• ENST00000789800.1:n.120+39111G>C

Variant summary

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

The ENST00000789800.1(ENSG00000302819):​n.120+39111G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,186 control chromosomes in the GnomAD database, including 42,931 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 0.75 (42931 hom., cov: 33)
• Consequence: ENSG00000302819 ENST00000789800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 1 publications found

Genes affected

ENSG00000302819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789800.1. 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
	ENSG00000302819	ENST00000789800.1		n.120+39111G>C		intron	N/A
	ENSG00000302819	ENST00000789804.1		n.370+29855G>C		intron	N/A
	ENSG00000302819	ENST00000789805.1		n.370+29855G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.750 AC: 114005 AN: 152068 Hom.: 42901 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.750 AC: 114091 AN: 152186 Hom.: 42931 Cov.: 33 AF XY: 0.751 AC XY: 55852 AN XY: 74396

African (AFR) AF: 0.818 AC: 33994 AN: 41542

American (AMR) AF: 0.699 AC: 10680 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2456 AN: 3472

East Asian (EAS) AF: 0.693 AC: 3585 AN: 5170

South Asian (SAS) AF: 0.776 AC: 3745 AN: 4826

European-Finnish (FIN) AF: 0.745 AC: 7891 AN: 10594

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49169 AN: 67984

Other (OTH) AF: 0.749 AC: 1585 AN: 2116

Alfa AF: 0.722 Hom.: 4966

Bravo AF: 0.746

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.65
PhyloP100		1.2

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: rs224001;

hg19: chr4-12935445;