11-128336515-C-T

Variant names:

• chr11-128336515-C-T
• rs6590322

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 0.514 in 152,068 control chromosomes in the GnomAD database, including 20,180 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 0.51 (20180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78100 AN: 151952 Hom.: 20169 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.514 AC: 78158 AN: 152068 Hom.: 20180 Cov.: 32 AF XY: 0.512 AC XY: 38060 AN XY: 74344

African (AFR) AF: 0.476 AC: 19746 AN: 41470

American (AMR) AF: 0.460 AC: 7035 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2558 AN: 5172

South Asian (SAS) AF: 0.547 AC: 2634 AN: 4816

European-Finnish (FIN) AF: 0.542 AC: 5739 AN: 10584

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36957 AN: 67950

Other (OTH) AF: 0.489 AC: 1029 AN: 2106

Alfa AF: 0.532 Hom.: 76814

Bravo AF: 0.506

Asia WGS AF: 0.558 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.54
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs6590322; hg19: chr11-128206410;