5-34259322-C-T

Variant names:

• chr5-34259322-C-T
• rs4866354
• ENST00000658746.1:n.135+13915C>T

Variant summary

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

The ENST00000658746.1(ENSG00000286543):​n.135+13915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,088 control chromosomes in the GnomAD database, including 54,802 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 0.82 (54802 hom., cov: 31)
• Consequence: ENSG00000286543 ENST00000658746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 1 publications found

Genes affected

ENSG00000286543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.966 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
ENSG00000286543	ENST00000658746.1	n.135+13915C>T		intron_variant	Intron 1 of 2
ENSG00000286543	ENST00000736918.1	n.237+13915C>T		intron_variant	Intron 1 of 1
ENSG00000286543	ENST00000736919.1	n.233+13915C>T		intron_variant	Intron 1 of 2
ENSG00000286543	ENST00000736921.1	n.166-6180C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124781 AN: 151970 Hom.: 54794 Cov.: 31

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.821 AC: 124821 AN: 152088 Hom.: 54802 Cov.: 31 AF XY: 0.823 AC XY: 61166 AN XY: 74334

African (AFR) AF: 0.471 AC: 19485 AN: 41406

American (AMR) AF: 0.931 AC: 14233 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4584 AN: 5170

South Asian (SAS) AF: 0.945 AC: 4555 AN: 4818

European-Finnish (FIN) AF: 0.902 AC: 9569 AN: 10604

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66116 AN: 68022

Other (OTH) AF: 0.864 AC: 1824 AN: 2112

Alfa AF: 0.872 Hom.: 11939

Bravo AF: 0.805

Asia WGS AF: 0.906 AC: 3148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.0
DANN	Benign	0.76
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4866354; hg19: chr5-34259427;