chr11-88428828-G-A

Variant names:

• chr11-88428828-G-A
• rs7935502

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 0.248 in 152,082 control chromosomes in the GnomAD database, including 5,176 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 0.25 (5176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.321 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: 0.248 AC: 37720 AN: 151964 Hom.: 5182 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.248 AC: 37702 AN: 152082 Hom.: 5176 Cov.: 32 AF XY: 0.240 AC XY: 17828 AN XY: 74336

African (AFR) AF: 0.144 AC: 5986 AN: 41480

American (AMR) AF: 0.271 AC: 4143 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3466

East Asian (EAS) AF: 0.0905 AC: 469 AN: 5180

South Asian (SAS) AF: 0.146 AC: 702 AN: 4820

European-Finnish (FIN) AF: 0.231 AC: 2441 AN: 10566

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22031 AN: 67968

Other (OTH) AF: 0.277 AC: 586 AN: 2112

Alfa AF: 0.301 Hom.: 31276

Bravo AF: 0.248

Asia WGS AF: 0.128 AC: 444 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	0.70
DANN	Benign	0.46
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7935502; hg19: chr11-88161996;