rs4766200

Variant names:

• chr12-4040383-A-G
• rs4766200
• ENST00000832971.1:n.151+3975A>G

Variant summary

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

The ENST00000832971.1(ENSG00000308279):​n.151+3975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 151,820 control chromosomes in the GnomAD database, including 2,671 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 0.17 (2671 hom., cov: 28)
• Consequence: ENSG00000308279 ENST00000832971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507
• Publications: 4 publications found

Genes affected

ENSG00000308279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832971.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308279	ENST00000832971.1		n.151+3975A>G		intron	N/A
	ENSG00000308279	ENST00000832972.1		n.179+3975A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25604 AN: 151702 Hom.: 2652 Cov.: 28

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.169 AC: 25656 AN: 151820 Hom.: 2671 Cov.: 28 AF XY: 0.170 AC XY: 12612 AN XY: 74184

African (AFR) AF: 0.125 AC: 5155 AN: 41384

American (AMR) AF: 0.223 AC: 3394 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2747 AN: 5154

South Asian (SAS) AF: 0.171 AC: 817 AN: 4786

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10550

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11054 AN: 67954

Other (OTH) AF: 0.164 AC: 345 AN: 2108

Alfa AF: 0.169 Hom.: 8188

Bravo AF: 0.184

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.47
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs4766200; hg19: chr12-4149549;