rs4865206

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986279	XR_001741689.1	n.195-12272G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287999	ENST00000660768.1	n.204-87484C>A		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.0736

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.233

Alfa AF: 0.248 Hom.: 2456

Bravo AF: 0.275

Asia WGS AF: 0.169 AC: 588 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	0.62
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4865206; hg19: chr4-53206994;