4-33061224-G-A

Variant names:

• chr4-33061224-G-A
• rs9990848
• ENST00000826125.1:n.-118C>T

Variant summary

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

The ENST00000826125.1(ENSG00000307412):​n.-118C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,726 control chromosomes in the GnomAD database, including 4,730 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 0.22 (4730 hom., cov: 32)
• Consequence: ENSG00000307412 ENST00000826125.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42
• Publications: 2 publications found

Genes affected

ENSG00000307412 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826125.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307412	ENST00000826125.1		n.-118C>T		upstream_gene	N/A
	ENSG00000307412	ENST00000826126.1		n.-118C>T		upstream_gene	N/A
	ENSG00000307412	ENST00000826127.1		n.-136C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33692 AN: 151608 Hom.: 4721 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.222 AC: 33735 AN: 151726 Hom.: 4730 Cov.: 32 AF XY: 0.222 AC XY: 16491 AN XY: 74160

African (AFR) AF: 0.361 AC: 14925 AN: 41358

American (AMR) AF: 0.267 AC: 4067 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1920 AN: 5090

South Asian (SAS) AF: 0.264 AC: 1271 AN: 4814

European-Finnish (FIN) AF: 0.0912 AC: 965 AN: 10584

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9161 AN: 67886

Other (OTH) AF: 0.258 AC: 545 AN: 2114

Alfa AF: 0.174 Hom.: 1089

Bravo AF: 0.241

Asia WGS AF: 0.399 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.050
DANN	Benign	0.71
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs9990848; hg19: chr4-33062846;