rs4865206

Variant names:

• chr4-52340828-G-T
• rs4865206
• ENST00000660768.1:n.204-87484C>A

Variant summary

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

The ENST00000660768.1(ENSG00000287999):​n.204-87484C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,066 control chromosomes in the GnomAD database, including 6,441 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 0.27 (6441 hom., cov: 32)
• Consequence: ENSG00000287999 ENST00000660768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 2 publications found

Genes affected

ENSG00000287999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660768.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287999	ENST00000660768.1		n.204-87484C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41485 AN: 151946 Hom.: 6436 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.273 AC: 41515 AN: 152066 Hom.: 6441 Cov.: 32 AF XY: 0.270 AC XY: 20089 AN XY: 74346

African (AFR) AF: 0.425 AC: 17644 AN: 41470

American (AMR) AF: 0.187 AC: 2862 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3472

East Asian (EAS) AF: 0.0736 AC: 380 AN: 5162

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4824

European-Finnish (FIN) AF: 0.233 AC: 2458 AN: 10556

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15221 AN: 67976

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.248 Hom.: 2731

Bravo AF: 0.275

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.37
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs4865206; hg19: chr4-53206994;