rs1783925

Positions:

• chr11-125434113-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.266 in 151,984 control chromosomes in the GnomAD database, including 6,090 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 (6090 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40409 AN: 151866 Hom.: 6089 Cov.: 30

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.266 AC: 40406 AN: 151984 Hom.: 6090 Cov.: 30 AF XY: 0.273 AC XY: 20256 AN XY: 74258

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.271

Alfa AF: 0.292 Hom.: 11165

Bravo AF: 0.263

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1783925; hg19: chr11-125304009; COSMIC: COSV53545401;