rs4859315

Variant names:

• chr4-33189747-T-C
• rs4859315
• ENST00000653925.1:n.38-12933T>C

Variant summary

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

The ENST00000653925.1(ENSG00000287968):​n.38-12933T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 152,234 control chromosomes in the GnomAD database, including 741 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 0.086 (741 hom., cov: 33)
• Consequence: ENSG00000287968 ENST00000653925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

Genes affected

ENSG00000287968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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
ENSG00000287968	ENST00000653925.1	n.38-12933T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13044 AN: 152114 Hom.: 744 Cov.: 33

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0856 AC: 13026 AN: 152234 Hom.: 741 Cov.: 33 AF XY: 0.0901 AC XY: 6703 AN XY: 74430

Gnomad4 AFR AF: 0.0238

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.0886

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0996 Hom.: 246

Bravo AF: 0.0751

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4859315; hg19: chr4-33191369;