11-13254782-C-T

Variant names:

• chr11-13254782-C-T
• rs10832008
• ENST00000787640.1:n.65+2831C>T

Variant summary

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

The ENST00000787640.1(ENSG00000302524):​n.65+2831C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,044 control chromosomes in the GnomAD database, including 1,940 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 0.15 (1940 hom., cov: 32)
• Consequence: ENSG00000302524 ENST00000787640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 5 publications found

Genes affected

ENSG00000302524 (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 = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787640.1. 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
	ENSG00000302524	ENST00000787640.1		n.65+2831C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23483 AN: 151926 Hom.: 1935 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.155 AC: 23515 AN: 152044 Hom.: 1940 Cov.: 32 AF XY: 0.159 AC XY: 11850 AN XY: 74314

African (AFR) AF: 0.143 AC: 5918 AN: 41476

American (AMR) AF: 0.152 AC: 2316 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1156 AN: 5172

South Asian (SAS) AF: 0.198 AC: 955 AN: 4822

European-Finnish (FIN) AF: 0.206 AC: 2170 AN: 10534

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9772 AN: 67990

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.144 Hom.: 7145

Bravo AF: 0.152

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.70
PhyloP100		0.38

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: rs10832008;

hg19: chr11-13276329;