rs4242084

Variant names:

• chr5-34259255-A-C
• rs4242084
• ENST00000658746.1:n.135+13848A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-34259255-A-C
• chr5-34259255-A-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+13848A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,136 control chromosomes in the GnomAD database, including 54,786 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 (54786 hom., cov: 32)
• Consequence: ENSG00000286543 ENST00000658746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• 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=-0.64).
• 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+13848A>C		intron_variant	Intron 1 of 2
ENSG00000286543	ENST00000736918.1	n.237+13848A>C		intron_variant	Intron 1 of 1
ENSG00000286543	ENST00000736919.1	n.233+13848A>C		intron_variant	Intron 1 of 2
ENSG00000286543	ENST00000736921.1	n.166-6247A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124770 AN: 152018 Hom.: 54778 Cov.: 32

Gnomad AFR AF: 0.470

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: 0.903

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.820 AC: 124810 AN: 152136 Hom.: 54786 Cov.: 32 AF XY: 0.823 AC XY: 61160 AN XY: 74354

African (AFR) AF: 0.470 AC: 19496 AN: 41474

American (AMR) AF: 0.931 AC: 14236 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4581 AN: 5168

South Asian (SAS) AF: 0.945 AC: 4553 AN: 4818

European-Finnish (FIN) AF: 0.903 AC: 9547 AN: 10578

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

European-Non Finnish (NFE) AF: 0.972 AC: 66119 AN: 68022

Other (OTH) AF: 0.863 AC: 1823 AN: 2112

Alfa AF: 0.831 Hom.: 9865

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	-0.64
CADD	Benign	3.9
DANN	Benign	0.58
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4242084; hg19: chr5-34259360;