rs4796870

Variant names:

• chr18-10129079-C-T
• rs4796870
• ENST00000582470.2:n.272+3578C>T

Variant summary

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

The ENST00000582470.2(ENSG00000265554):​n.272+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 ENST00000582470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 4 publications found

Genes affected

ENSG00000265554 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582470.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000265554	ENST00000582470.2	TSL:3	n.272+3578C>T		intron	N/A
	ENSG00000265554	ENST00000669473.1		n.422+3578C>T		intron	N/A
	ENSG00000265554	ENST00000685786.1		n.389-15078C>T		intron	N/A

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

African (AFR) AF: 0.112 AC: 4661 AN: 41508

American (AMR) AF: 0.236 AC: 3614 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3472

East Asian (EAS) AF: 0.125 AC: 644 AN: 5156

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4814

European-Finnish (FIN) AF: 0.222 AC: 2342 AN: 10558

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14210 AN: 68006

Other (OTH) AF: 0.176 AC: 373 AN: 2116

Alfa AF: 0.198 Hom.: 3822

Bravo AF: 0.179

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4796870; hg19: chr18-10129076;