ENST00000654542.1:n.84+9303T>C

Variant names:

• chr3-127209087-A-G
• rs13099725
• ENST00000654542.1:n.84+9303T>C

Variant summary

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

The ENST00000654542.1(ENSG00000287784):​n.84+9303T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,320 control chromosomes in the GnomAD database, including 979 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 0.10 (979 hom., cov: 33)
• Consequence: ENSG00000287784 ENST00000654542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• 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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 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

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
	ENSG00000287784	ENST00000654542.1		n.84+9303T>C		intron	N/A
	ENSG00000287784	ENST00000827470.1		n.197-4775T>C		intron	N/A
	ENSG00000287784	ENST00000827471.1		n.215-4775T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15307 AN: 152202 Hom.: 976 Cov.: 33

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.0927

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.101 AC: 15334 AN: 152320 Hom.: 979 Cov.: 33 AF XY: 0.102 AC XY: 7559 AN XY: 74466

African (AFR) AF: 0.0280 AC: 1166 AN: 41582

American (AMR) AF: 0.135 AC: 2065 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1323 AN: 5182

South Asian (SAS) AF: 0.0936 AC: 452 AN: 4828

European-Finnish (FIN) AF: 0.114 AC: 1214 AN: 10608

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8538 AN: 68022

Other (OTH) AF: 0.105 AC: 223 AN: 2116

Alfa AF: 0.116 Hom.: 746

Bravo AF: 0.102

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.4
DANN	Benign	0.87
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs13099725; hg19: chr3-126927930;