ENST00000659320.1:n.216-54459T>C

Variant names:

• chr4-32639755-A-G
• rs2166277
• ENST00000659320.1:n.216-54459T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659320.1(ENSG00000286784):​n.216-54459T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,226 control chromosomes in the GnomAD database, including 2,051 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 (2051 hom., cov: 33)
• Consequence: ENSG00000286784 ENST00000659320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

ENSG00000286784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286784	ENST00000659320.1	n.216-54459T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15837 AN: 152106 Hom.: 2049 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.00870

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.104 AC: 15864 AN: 152226 Hom.: 2051 Cov.: 33 AF XY: 0.103 AC XY: 7658 AN XY: 74416

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.0282

Gnomad4 NFE AF: 0.00870

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0638 Hom.: 143

Bravo AF: 0.118

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2166277; hg19: chr4-32641377;