chr11-15747106-C-T

Variant names:

• chr11-15747106-C-T
• rs10832515
• ENST00000524613.1:n.187+11606G>A

Variant summary

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

The ENST00000524613.1(ENSG00000254645):​n.187+11606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,156 control chromosomes in the GnomAD database, including 4,655 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 0.23 (4655 hom., cov: 32)
• Consequence: ENSG00000254645 ENST00000524613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 3 publications found

Genes affected

ENSG00000254645 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524613.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254645	ENST00000524613.1	TSL:5	n.187+11606G>A		intron	N/A
	ENSG00000254645	ENST00000663676.1		n.184+11606G>A		intron	N/A
	ENSG00000254645	ENST00000727850.1		n.174+11606G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35316 AN: 152038 Hom.: 4653 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.232 AC: 35331 AN: 152156 Hom.: 4655 Cov.: 32 AF XY: 0.235 AC XY: 17452 AN XY: 74366

African (AFR) AF: 0.0995 AC: 4134 AN: 41534

American (AMR) AF: 0.215 AC: 3294 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 963 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1966 AN: 5170

South Asian (SAS) AF: 0.184 AC: 886 AN: 4824

European-Finnish (FIN) AF: 0.372 AC: 3924 AN: 10562

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19354 AN: 67982

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.239 Hom.: 799

Bravo AF: 0.216

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.62
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10832515; hg19: chr11-15768652;