rs10466455

Variant names:

• chr11-34759389-T-C
• rs10466455
• ENST00000843048.1:n.656+4782T>C

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.656+4782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,890 control chromosomes in the GnomAD database, including 11,717 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 0.39 (11717 hom., cov: 31)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 18 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843048.1. 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
	ENSG00000309692	ENST00000843048.1		n.656+4782T>C		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.848+4782T>C		intron	N/A
	ENSG00000309692	ENST00000843050.1		n.440+4782T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59406 AN: 151772 Hom.: 11710 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.391 AC: 59441 AN: 151890 Hom.: 11717 Cov.: 31 AF XY: 0.391 AC XY: 28996 AN XY: 74212

African (AFR) AF: 0.386 AC: 16010 AN: 41438

American (AMR) AF: 0.322 AC: 4908 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2230 AN: 5172

South Asian (SAS) AF: 0.357 AC: 1719 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4631 AN: 10520

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27554 AN: 67910

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.394 Hom.: 10035

Bravo AF: 0.381

Asia WGS AF: 0.396 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.60
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10466455;

hg19: chr11-34780936;