chr11-117103213-G-C

Position:

• chr11-117103213-G-C

Variant summary

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

The variant allele was found at a frequency of 0.413 in 151,816 control chromosomes in the GnomAD database, including 15,108 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 0.41 (15107 hom., cov: 31)
  • Exomes 𝑓: 0.35 (1 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117103213G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000224077	ENST00000442124.1	n.165-11G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62583 AN: 151672 Hom.: 15070 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.346 AC: 9 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 6 AN XY: 20

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.413 AC: 62667 AN: 151790 Hom.: 15107 Cov.: 31 AF XY: 0.414 AC XY: 30673 AN XY: 74152

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.358

Alfa AF: 0.193 Hom.: 398

Bravo AF: 0.423

Asia WGS AF: 0.395 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12269901; hg19: chr11-116973929;