rs728425

Variant names:

• chr14-54116469-T-C
• rs728425
• ENST00000747857.1:n.595-24372A>G

Variant summary

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

The ENST00000747857.1(ENSG00000297427):​n.595-24372A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,044 control chromosomes in the GnomAD database, including 25,635 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 0.55 (25635 hom., cov: 32)
• Consequence: ENSG00000297427 ENST00000747857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 3 publications found

Genes affected

ENSG00000297427 (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 (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747857.1. 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
	ENSG00000297427	ENST00000747857.1		n.595-24372A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83622 AN: 151926 Hom.: 25636 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.550 AC: 83631 AN: 152044 Hom.: 25635 Cov.: 32 AF XY: 0.556 AC XY: 41299 AN XY: 74328

African (AFR) AF: 0.259 AC: 10730 AN: 41494

American (AMR) AF: 0.558 AC: 8509 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2482 AN: 5158

South Asian (SAS) AF: 0.674 AC: 3245 AN: 4818

European-Finnish (FIN) AF: 0.750 AC: 7943 AN: 10596

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46493 AN: 67958

Other (OTH) AF: 0.572 AC: 1208 AN: 2112

Alfa AF: 0.647 Hom.: 15324

Bravo AF: 0.519

Asia WGS AF: 0.572 AC: 1988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.73
DANN	Benign	0.72
PhyloP100		-1.0

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: rs728425;

hg19: chr14-54583187;