4-4933478-G-A

Variant names:

• chr4-4933478-G-A
• rs4689963
• ENST00000774609.1:n.142-342G>A

Variant summary

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

The NR_125893.1(LOC101928306):​n.354-342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,180 control chromosomes in the GnomAD database, including 45,082 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 0.77 (45082 hom., cov: 32)
• Consequence: LOC101928306 NR_125893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 1 publications found

Genes affected

ENSG00000300857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125893.1. 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
	LOC101928306	NR_125893.1		n.354-342G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300857	ENST00000774609.1		n.142-342G>A		intron	N/A
	ENSG00000300857	ENST00000774610.1		n.165-342G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116523 AN: 152062 Hom.: 45020 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.766 AC: 116645 AN: 152180 Hom.: 45082 Cov.: 32 AF XY: 0.774 AC XY: 57628 AN XY: 74416

African (AFR) AF: 0.843 AC: 35007 AN: 41530

American (AMR) AF: 0.811 AC: 12393 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3470

East Asian (EAS) AF: 0.898 AC: 4644 AN: 5174

South Asian (SAS) AF: 0.842 AC: 4064 AN: 4824

European-Finnish (FIN) AF: 0.789 AC: 8362 AN: 10598

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47306 AN: 67976

Other (OTH) AF: 0.757 AC: 1601 AN: 2116

Alfa AF: 0.720 Hom.: 24857

Bravo AF: 0.768

Asia WGS AF: 0.851 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.067
DANN	Benign	0.40
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs4689963; hg19: chr4-4935205;