rs10832515

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376567	XR_001748140.2	n.259+21112G>A		intron_variant	Intron 1 of 6
LOC105376567	XR_001748141.2	n.259+21112G>A		intron_variant	Intron 1 of 4
LOC105376567	XR_002957238.2	n.259+21112G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254645	ENST00000524613.1	n.187+11606G>A		intron_variant	Intron 1 of 8	5
ENSG00000254645	ENST00000663676.1	n.184+11606G>A		intron_variant	Intron 1 of 7
ENSG00000254645	ENST00000727850.1	n.174+11606G>A		intron_variant	Intron 1 of 3

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 v4.3

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;