11-128827168-C-T

Variant names:

• chr11-128827168-C-T
• rs677035

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 0.104 in 152,182 control chromosomes in the GnomAD database, including 850 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 0.10 (850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15786 AN: 152062 Hom.: 846 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0875

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

GnomAD4 genome AF: 0.104 AC: 15805 AN: 152182 Hom.: 850 Cov.: 32 AF XY: 0.104 AC XY: 7747 AN XY: 74402

African (AFR) AF: 0.102 AC: 4230 AN: 41508

American (AMR) AF: 0.0597 AC: 913 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3470

East Asian (EAS) AF: 0.0953 AC: 494 AN: 5186

South Asian (SAS) AF: 0.149 AC: 716 AN: 4806

European-Finnish (FIN) AF: 0.131 AC: 1394 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7442 AN: 67988

Other (OTH) AF: 0.0875 AC: 185 AN: 2114

Alfa AF: 0.105 Hom.: 1275

Bravo AF: 0.0970

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.95
DANN	Benign	0.57
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs677035; hg19: chr11-128697063;