chr11-128021095-G-T

Position:

• chr11-128021095-G-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 0.441 in 151,984 control chromosomes in the GnomAD database, including 15,916 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 0.44 (15916 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67003 AN: 151864 Hom.: 15902 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.441 AC: 67058 AN: 151984 Hom.: 15916 Cov.: 31 AF XY: 0.433 AC XY: 32157 AN XY: 74266

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.0760

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.454

Alfa AF: 0.417 Hom.: 2835

Bravo AF: 0.449

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.051
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1863372; hg19: chr11-127890990;