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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723568	XR_007062652.1	n.1044+4782T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309692	ENST00000843048.1	n.656+4782T>C		intron_variant	Intron 2 of 2
ENSG00000309692	ENST00000843049.1	n.848+4782T>C		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843050.1	n.440+4782T>C		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843051.1	n.298+4782T>C		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs10466455; hg19: chr11-34780936;