rs10832515

Positions:

• chr11-15747106-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663676.1(ENSG00000254645):​n.184+11606G>A variant causes a intron, non coding transcript 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: ENST00000663676.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105376567	XR_001748141.2	n.259+21112G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663676.1	n.184+11606G>A		intron_variant, non_coding_transcript_variant
	ENST00000524613.1	n.187+11606G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.238

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10832515; hg19: chr11-15768652;