11-124838802-A-G

Variant names:

• chr11-124838802-A-G
• rs610104

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 0.275 in 151,960 control chromosomes in the GnomAD database, including 6,155 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 0.27 (6155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 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: 0.275 AC: 41696 AN: 151842 Hom.: 6149 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.275 AC: 41734 AN: 151960 Hom.: 6155 Cov.: 32 AF XY: 0.266 AC XY: 19726 AN XY: 74280

African (AFR) AF: 0.343 AC: 14211 AN: 41408

American (AMR) AF: 0.223 AC: 3406 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3470

East Asian (EAS) AF: 0.0345 AC: 178 AN: 5156

South Asian (SAS) AF: 0.130 AC: 627 AN: 4816

European-Finnish (FIN) AF: 0.239 AC: 2528 AN: 10566

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18580 AN: 67970

Other (OTH) AF: 0.291 AC: 614 AN: 2108

Alfa AF: 0.274 Hom.: 12265

Bravo AF: 0.279

Asia WGS AF: 0.0940 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.024
DANN	Benign	0.47
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs610104; hg19: chr11-124708698;