rs11024460

Variant names:

• chr11-18062635-C-T
• rs11024460
• ENST00000787024.1:n.97-2413C>T

Variant summary

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

The ENST00000787024.1(ENSG00000302464):​n.97-2413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,110 control chromosomes in the GnomAD database, including 3,029 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 0.18 (3029 hom., cov: 32)
• Consequence: ENSG00000302464 ENST00000787024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 7 publications found

Genes affected

ENSG00000302464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787024.1. 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
	ENSG00000302464	ENST00000787024.1		n.97-2413C>T		intron	N/A
	ENSG00000302464	ENST00000787025.1		n.194+601C>T		intron	N/A
	ENSG00000302464	ENST00000787026.1		n.190+601C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26664 AN: 151992 Hom.: 3029 Cov.: 32

Gnomad AFR AF: 0.0527

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.175 AC: 26666 AN: 152110 Hom.: 3029 Cov.: 32 AF XY: 0.176 AC XY: 13075 AN XY: 74334

African (AFR) AF: 0.0525 AC: 2180 AN: 41526

American (AMR) AF: 0.154 AC: 2360 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3472

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5188

South Asian (SAS) AF: 0.135 AC: 650 AN: 4820

European-Finnish (FIN) AF: 0.283 AC: 2980 AN: 10544

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17002 AN: 67962

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.210 Hom.: 5509

Bravo AF: 0.164

Asia WGS AF: 0.0730 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.59
PhyloP100		-0.83

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: rs11024460;

hg19: chr11-18084182;