11-47585583-C-T

Variant names:

• chr11-47585583-C-T
• rs10838731

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 0.227 in 151,430 control chromosomes in the GnomAD database, including 4,999 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 0.23 (4999 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34407 AN: 151314 Hom.: 5002 Cov.: 28

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.227 AC: 34395 AN: 151430 Hom.: 4999 Cov.: 28 AF XY: 0.227 AC XY: 16776 AN XY: 73928

African (AFR) AF: 0.0565 AC: 2332 AN: 41310

American (AMR) AF: 0.222 AC: 3366 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1173 AN: 3464

East Asian (EAS) AF: 0.347 AC: 1777 AN: 5116

South Asian (SAS) AF: 0.456 AC: 2178 AN: 4776

European-Finnish (FIN) AF: 0.217 AC: 2269 AN: 10450

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20466 AN: 67820

Other (OTH) AF: 0.274 AC: 576 AN: 2100

Alfa AF: 0.130 Hom.: 250

Bravo AF: 0.215

Asia WGS AF: 0.396 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10838731; hg19: chr11-47607135;