ENST00000754158.1:n.108-2254A>C

Variant names:

• chr4-11083057-A-C
• rs951881
• ENST00000754158.1:n.108-2254A>C

Variant summary

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

The ENST00000754158.1(ENSG00000298262):​n.108-2254A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,194 control chromosomes in the GnomAD database, including 3,098 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 0.19 (3098 hom., cov: 32)
• Consequence: ENSG00000298262 ENST00000754158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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.108-2254A>C		intron	N/A
	ENSG00000298262	ENST00000754159.1		n.494+16114A>C		intron	N/A
	ENSG00000298262	ENST00000754160.1		n.486+16114A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28245 AN: 152076 Hom.: 3074 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.186 AC: 28325 AN: 152194 Hom.: 3098 Cov.: 32 AF XY: 0.188 AC XY: 14018 AN XY: 74430

African (AFR) AF: 0.297 AC: 12309 AN: 41484

American (AMR) AF: 0.183 AC: 2793 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.147 AC: 763 AN: 5186

South Asian (SAS) AF: 0.184 AC: 889 AN: 4828

European-Finnish (FIN) AF: 0.169 AC: 1797 AN: 10614

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

European-Non Finnish (NFE) AF: 0.128 AC: 8679 AN: 68000

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.127 Hom.: 708

Bravo AF: 0.193

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.6
DANN	Benign	0.71
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs951881; hg19: chr4-11084681;