rs10866307

Variant names:

• chr4-188372532-C-T
• rs10866307
• ENST00000807121.1:n.421-13754G>A

Variant summary

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

The ENST00000807121.1(ENSG00000304922):​n.421-13754G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,162 control chromosomes in the GnomAD database, including 538 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 0.056 (538 hom., cov: 33)
• Consequence: ENSG00000304922 ENST00000807121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 2 publications found

Genes affected

ENSG00000304922 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807121.1. 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
	ENSG00000304922	ENST00000807121.1		n.421-13754G>A		intron	N/A
	ENSG00000304922	ENST00000807122.1		n.386-13754G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8564 AN: 152044 Hom.: 535 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.0337

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

GnomAD4 genome AF: 0.0565 AC: 8593 AN: 152162 Hom.: 538 Cov.: 33 AF XY: 0.0612 AC XY: 4550 AN XY: 74404

African (AFR) AF: 0.118 AC: 4912 AN: 41516

American (AMR) AF: 0.0702 AC: 1072 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1277 AN: 5156

South Asian (SAS) AF: 0.0586 AC: 283 AN: 4830

European-Finnish (FIN) AF: 0.0760 AC: 805 AN: 10596

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.00237 AC: 161 AN: 68012

Other (OTH) AF: 0.0347 AC: 73 AN: 2102

Alfa AF: 0.0263 Hom.: 48

Bravo AF: 0.0601

Asia WGS AF: 0.169 AC: 586 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.21
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs10866307; hg19: chr4-189293686;