ENST00000654542.1:n.84+3991C>T

Variant names:

• chr3-127214399-G-A
• rs4679351
• ENST00000654542.1:n.84+3991C>T

Variant summary

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

The ENST00000654542.1(ENSG00000287784):​n.84+3991C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,096 control chromosomes in the GnomAD database, including 44,348 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 0.75 (44348 hom., cov: 33)
• Consequence: ENSG00000287784 ENST00000654542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 3 publications found

Genes affected

ENSG00000287784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654542.1. 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
	ENSG00000287784	ENST00000654542.1		n.84+3991C>T		intron	N/A
	ENSG00000287784	ENST00000827470.1		n.196+3991C>T		intron	N/A
	ENSG00000287784	ENST00000827471.1		n.214+3954C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113510 AN: 151978 Hom.: 44336 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.747 AC: 113560 AN: 152096 Hom.: 44348 Cov.: 33 AF XY: 0.752 AC XY: 55880 AN XY: 74346

African (AFR) AF: 0.492 AC: 20366 AN: 41436

American (AMR) AF: 0.835 AC: 12757 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2785 AN: 3468

East Asian (EAS) AF: 0.839 AC: 4354 AN: 5190

South Asian (SAS) AF: 0.834 AC: 4014 AN: 4814

European-Finnish (FIN) AF: 0.861 AC: 9116 AN: 10586

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57456 AN: 68000

Other (OTH) AF: 0.770 AC: 1625 AN: 2110

Alfa AF: 0.810 Hom.: 8650

Bravo AF: 0.733

Asia WGS AF: 0.787 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4679351; hg19: chr3-126933242;