ENST00000727128.1:n.187+15223A>G

Variant names:

• chr3-186537043-A-G
• rs1447670
• ENST00000727128.1:n.187+15223A>G

Variant summary

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

The ENST00000727128.1(ENSG00000294974):​n.187+15223A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,134 control chromosomes in the GnomAD database, including 4,072 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 0.21 (4072 hom., cov: 32)
• Consequence: ENSG00000294974 ENST00000727128.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 8 publications found

Genes affected

ENSG00000294974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727128.1. 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
	ENSG00000294974	ENST00000727128.1		n.187+15223A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32267 AN: 152016 Hom.: 4064 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.212 AC: 32295 AN: 152134 Hom.: 4072 Cov.: 32 AF XY: 0.215 AC XY: 16005 AN XY: 74364

African (AFR) AF: 0.346 AC: 14348 AN: 41450

American (AMR) AF: 0.204 AC: 3126 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3470

East Asian (EAS) AF: 0.133 AC: 687 AN: 5180

South Asian (SAS) AF: 0.230 AC: 1108 AN: 4820

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10592

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9635 AN: 68014

Other (OTH) AF: 0.220 AC: 465 AN: 2114

Alfa AF: 0.164 Hom.: 6793

Bravo AF: 0.217

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1447670;

hg19: chr3-186254832;