chr11-1207775-A-G

Variant names:

• chr11-1207775-A-G
• rs28678421

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 0.262 in 152,142 control chromosomes in the GnomAD database, including 5,801 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 0.26 (5801 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.262 AC: 39841 AN: 152024 Hom.: 5784 Cov.: 34

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.262 AC: 39899 AN: 152142 Hom.: 5801 Cov.: 34 AF XY: 0.261 AC XY: 19389 AN XY: 74372

African (AFR) AF: 0.392 AC: 16290 AN: 41516

American (AMR) AF: 0.178 AC: 2715 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.100 AC: 517 AN: 5164

South Asian (SAS) AF: 0.236 AC: 1139 AN: 4826

European-Finnish (FIN) AF: 0.254 AC: 2689 AN: 10606

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15117 AN: 67956

Other (OTH) AF: 0.267 AC: 563 AN: 2112

Alfa AF: 0.231 Hom.: 5859

Bravo AF: 0.258

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.25
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs28678421; hg19: chr11-1229005;