chr4-106906118-G-A

Variant names:

• chr4-106906118-G-A
• rs12186280
• ENST00000650850.1:n.486-4940G>A

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.486-4940G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0435 in 152,174 control chromosomes in the GnomAD database, including 232 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 0.043 (232 hom., cov: 32)
• Consequence: ENSG00000286147 ENST00000650850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

ENSG00000286147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0602 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
ENSG00000286147	ENST00000650850.1	n.486-4940G>A		intron_variant	Intron 6 of 10

Frequencies

GnomAD3 genomes AF: 0.0435 AC: 6614 AN: 152056 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0435 AC: 6612 AN: 152174 Hom.: 232 Cov.: 32 AF XY: 0.0414 AC XY: 3078 AN XY: 74398

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0553

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0617

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.0603 Hom.: 182

Bravo AF: 0.0458

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12186280; hg19: chr4-107827275;