4-147308510-C-T

Variant names:

• chr4-147308510-C-T
• rs2714888
• ENST00000754810.1:n.266+376C>T

Variant summary

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

The ENST00000754810.1(ENSG00000298313):​n.266+376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,970 control chromosomes in the GnomAD database, including 8,063 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 0.27 (8063 hom., cov: 32)
• Consequence: ENSG00000298313 ENST00000754810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860
• Publications: 5 publications found

Genes affected

ENSG00000298313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754810.1. 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
	ENSG00000298313	ENST00000754810.1		n.266+376C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41488 AN: 151852 Hom.: 8035 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.274 AC: 41569 AN: 151970 Hom.: 8063 Cov.: 32 AF XY: 0.270 AC XY: 20054 AN XY: 74270

African (AFR) AF: 0.548 AC: 22698 AN: 41436

American (AMR) AF: 0.234 AC: 3564 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3470

East Asian (EAS) AF: 0.115 AC: 594 AN: 5162

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4810

European-Finnish (FIN) AF: 0.126 AC: 1337 AN: 10584

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10892 AN: 67950

Other (OTH) AF: 0.253 AC: 533 AN: 2108

Alfa AF: 0.160 Hom.: 1085

Bravo AF: 0.292

Asia WGS AF: 0.262 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.62
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs2714888; hg19: chr4-148229662;