4-32639002-A-C

Variant names:

• chr4-32639002-A-C
• rs1822923
• ENST00000659320.1:n.216-53706T>G

Variant summary

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

The ENST00000659320.1(ENSG00000286784):​n.216-53706T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,102 control chromosomes in the GnomAD database, including 45,105 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 0.76 (45105 hom., cov: 32)
• Consequence: ENSG00000286784 ENST00000659320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 2 publications found

Genes affected

ENSG00000286784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659320.1. 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
	ENSG00000286784	ENST00000659320.1		n.216-53706T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116143 AN: 151984 Hom.: 45059 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.764 AC: 116245 AN: 152102 Hom.: 45105 Cov.: 32 AF XY: 0.763 AC XY: 56677 AN XY: 74314

African (AFR) AF: 0.869 AC: 36074 AN: 41500

American (AMR) AF: 0.809 AC: 12359 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2590 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4751 AN: 5168

South Asian (SAS) AF: 0.849 AC: 4088 AN: 4816

European-Finnish (FIN) AF: 0.578 AC: 6114 AN: 10582

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47898 AN: 67974

Other (OTH) AF: 0.750 AC: 1586 AN: 2116

Alfa AF: 0.732 Hom.: 107977

Bravo AF: 0.784

Asia WGS AF: 0.895 AC: 3109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1822923; hg19: chr4-32640624;