rs4796870

Variant names:

• chr18-10129079-C-T
• rs4796870
• ENST00000582470.1:n.162+3578C>T

Variant summary

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

The ENST00000582470.1(ENSG00000265554):​n.162+3578C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,130 control chromosomes in the GnomAD database, including 2,716 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 0.18 (2716 hom., cov: 32)
• Consequence: ENSG00000265554 ENST00000582470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

ENSG00000265554 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 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
ENSG00000265554	ENST00000582470.1	n.162+3578C>T		intron_variant	Intron 1 of 1	3
ENSG00000265554	ENST00000669473.1	n.422+3578C>T		intron_variant	Intron 2 of 2
ENSG00000265554	ENST00000685786.1	n.389-15078C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27760 AN: 152012 Hom.: 2715 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.183 AC: 27777 AN: 152130 Hom.: 2716 Cov.: 32 AF XY: 0.183 AC XY: 13625 AN XY: 74340

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.176

Alfa AF: 0.201 Hom.: 2929

Bravo AF: 0.179

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4796870; hg19: chr18-10129076;