ENST00000754133.1:n.304+14786T>G

Variant names:

• chr2-154524263-T-G
• rs1830018
• ENST00000754133.1:n.304+14786T>G

Variant summary

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

The ENST00000754133.1(ENSG00000298255):​n.304+14786T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,074 control chromosomes in the GnomAD database, including 2,762 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 (2762 hom., cov: 32)
• Consequence: ENSG00000298255 ENST00000754133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 2 publications found

Genes affected

ENSG00000298255 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754133.1. 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
	ENSG00000298255	ENST00000754133.1		n.304+14786T>G		intron	N/A
	ENSG00000298255	ENST00000754134.1		n.250+37213T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25763 AN: 151956 Hom.: 2751 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.170 AC: 25788 AN: 152074 Hom.: 2762 Cov.: 32 AF XY: 0.172 AC XY: 12821 AN XY: 74328

African (AFR) AF: 0.0510 AC: 2120 AN: 41528

American (AMR) AF: 0.253 AC: 3862 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3468

East Asian (EAS) AF: 0.454 AC: 2342 AN: 5158

South Asian (SAS) AF: 0.183 AC: 882 AN: 4818

European-Finnish (FIN) AF: 0.180 AC: 1909 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13457 AN: 67918

Other (OTH) AF: 0.196 AC: 414 AN: 2116

Alfa AF: 0.0900 Hom.: 154

Bravo AF: 0.173

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.8
DANN	Benign	0.85
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1830018; hg19: chr2-155380775;