chr11-127027082-C-T

Position:

• chr11-127027082-C-T

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 0.354 in 152,108 control chromosomes in the GnomAD database, including 10,123 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 0.35 (10123 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127027082C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000255087	ENST00000530177.2	n.154+5175C>T		intron_variant		4
ENSG00000255087	ENST00000647195.1	n.143+5175C>T		intron_variant
ENSG00000255087	ENST00000654157.1	n.150+5175C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53771 AN: 151990 Hom.: 10111 Cov.: 33

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53830 AN: 152108 Hom.: 10123 Cov.: 33 AF XY: 0.360 AC XY: 26787 AN XY: 74354

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.324

Alfa AF: 0.308 Hom.: 1878

Bravo AF: 0.354

Asia WGS AF: 0.321 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs503397; hg19: chr11-126896977;