11-117138230-T-C

Position:

• chr11-117138230-T-C

Variant summary

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

The ENST00000528464.1(ENSG00000254851):​n.470T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 142,668 control chromosomes in the GnomAD database, including 33,877 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 0.65 (33877 hom., cov: 22)
  • Exomes 𝑓: 0.76 (380610 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000528464.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000528464.1	n.470T>C		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.653 AC: 93088 AN: 142546 Hom.: 33875 Cov.: 22

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.672

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.763 AC: 937368 AN: 1228860 Hom.: 380610 Cov.: 22 AF XY: 0.756 AC XY: 459805 AN XY: 607878

Gnomad4 AFR exome AF: 0.394

Gnomad4 AMR exome AF: 0.672

Gnomad4 ASJ exome AF: 0.706

Gnomad4 EAS exome AF: 0.419

Gnomad4 SAS exome AF: 0.491

Gnomad4 FIN exome AF: 0.754

Gnomad4 NFE exome AF: 0.814

Gnomad4 OTH exome AF: 0.722

GnomAD4 genome AF: 0.653 AC: 93116 AN: 142668 Hom.: 33877 Cov.: 22 AF XY: 0.643 AC XY: 44508 AN XY: 69252

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.667

Alfa AF: 0.716 Hom.: 4699

Asia WGS AF: 0.421 AC: 1435 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs504068; hg19: chr11-117008946;