11-128021095-G-T

Variant names:

• chr11-128021095-G-T
• rs1863372

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.596 AC: 24715 AN: 41434

American (AMR) AF: 0.372 AC: 5685 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3468

East Asian (EAS) AF: 0.0760 AC: 393 AN: 5174

South Asian (SAS) AF: 0.392 AC: 1879 AN: 4796

European-Finnish (FIN) AF: 0.387 AC: 4082 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27365 AN: 67972

Other (OTH) AF: 0.454 AC: 957 AN: 2108

Alfa AF: 0.413 Hom.: 22954

Bravo AF: 0.449

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.051
DANN	Benign	0.35
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1863372; hg19: chr11-127890990;