chr11-102875061-T-C

Position:

• chr11-102875061-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.108 in 600,826 control chromosomes in the GnomAD database, including 4,255 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 0.092 (921 hom., cov: 33)
  • Exomes 𝑓: 0.11 (3334 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102875061T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14026 AN: 152134 Hom.: 920 Cov.: 33

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0908

GnomAD4 exome AF: 0.114 AC: 50958 AN: 448574 Hom.: 3334 Cov.: 5 AF XY: 0.112 AC XY: 26458 AN XY: 235810

Gnomad4 AFR exome AF: 0.0223

Gnomad4 AMR exome AF: 0.0625

Gnomad4 ASJ exome AF: 0.115

Gnomad4 EAS exome AF: 0.0223

Gnomad4 SAS exome AF: 0.0802

Gnomad4 FIN exome AF: 0.179

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.0921 AC: 14027 AN: 152252 Hom.: 921 Cov.: 33 AF XY: 0.0935 AC XY: 6961 AN XY: 74432

Gnomad4 AFR AF: 0.0224

Gnomad4 AMR AF: 0.0700

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0238

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0744 Hom.: 107

Bravo AF: 0.0790

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	16
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2276109; hg19: chr11-102745791;