4-11080525-T-A

Variant names:

• chr4-11080525-T-A
• rs7685923
• ENST00000754158.1:n.108-4786T>A

Variant summary

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

The ENST00000754158.1(ENSG00000298262):​n.108-4786T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 150,630 control chromosomes in the GnomAD database, including 2,985 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 0.18 (2985 hom., cov: 30)
• Consequence: ENSG00000298262 ENST00000754158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 5 publications found

Genes affected

ENSG00000298262 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754158.1. 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
	ENSG00000298262	ENST00000754158.1		n.108-4786T>A		intron	N/A
	ENSG00000298262	ENST00000754159.1		n.494+13582T>A		intron	N/A
	ENSG00000298262	ENST00000754160.1		n.486+13582T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27675 AN: 150544 Hom.: 2962 Cov.: 30

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.184 AC: 27746 AN: 150630 Hom.: 2985 Cov.: 30 AF XY: 0.186 AC XY: 13676 AN XY: 73470

African (AFR) AF: 0.293 AC: 12002 AN: 40914

American (AMR) AF: 0.181 AC: 2748 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3456

East Asian (EAS) AF: 0.147 AC: 755 AN: 5136

South Asian (SAS) AF: 0.184 AC: 875 AN: 4768

European-Finnish (FIN) AF: 0.163 AC: 1648 AN: 10096

Middle Eastern (MID) AF: 0.171 AC: 49 AN: 286

European-Non Finnish (NFE) AF: 0.127 AC: 8633 AN: 67794

Other (OTH) AF: 0.193 AC: 404 AN: 2094

Alfa AF: 0.165 Hom.: 277

Bravo AF: 0.192

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.8
DANN	Benign	0.74
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs7685923; hg19: chr4-11082149;