11-57879836-G-C

Variant names:

• chr11-57879836-G-C
• rs1704781

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 0.292 in 151,926 control chromosomes in the GnomAD database, including 7,573 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 0.29 (7573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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: 0.292 AC: 44276 AN: 151810 Hom.: 7562 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.292 AC: 44299 AN: 151926 Hom.: 7573 Cov.: 32 AF XY: 0.304 AC XY: 22579 AN XY: 74244

African (AFR) AF: 0.227 AC: 9417 AN: 41436

American (AMR) AF: 0.429 AC: 6547 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1118 AN: 3458

East Asian (EAS) AF: 0.779 AC: 4022 AN: 5160

South Asian (SAS) AF: 0.350 AC: 1684 AN: 4812

European-Finnish (FIN) AF: 0.334 AC: 3526 AN: 10554

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16988 AN: 67950

Other (OTH) AF: 0.296 AC: 622 AN: 2102

Alfa AF: 0.265 Hom.: 742

Bravo AF: 0.302

Asia WGS AF: 0.574 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.82
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1704781; hg19: chr11-57647308;