11-129354771-T-G

Variant names:

• chr11-129354771-T-G
• rs1027323

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 0.397 in 151,884 control chromosomes in the GnomAD database, including 13,136 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 0.40 (13136 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.511 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: 0.397 AC: 60276 AN: 151766 Hom.: 13115 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.397 AC: 60308 AN: 151884 Hom.: 13136 Cov.: 31 AF XY: 0.402 AC XY: 29798 AN XY: 74208

African (AFR) AF: 0.214 AC: 8876 AN: 41450

American (AMR) AF: 0.521 AC: 7944 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1674 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2499 AN: 5110

South Asian (SAS) AF: 0.509 AC: 2445 AN: 4808

European-Finnish (FIN) AF: 0.463 AC: 4880 AN: 10544

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30644 AN: 67934

Other (OTH) AF: 0.423 AC: 891 AN: 2108

Alfa AF: 0.441 Hom.: 15582

Bravo AF: 0.394

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.50
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs1027323; hg19: chr11-129224666;