rs578784

chr11-112129580-G-A

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 0.262 in 152,122 control chromosomes in the GnomAD database, including 5,377 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 (5377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39878 AN: 152004 Hom.: 5381 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.262 AC: 39863 AN: 152122 Hom.: 5377 Cov.: 32 AF XY: 0.260 AC XY: 19322 AN XY: 74366

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.254

Alfa AF: 0.276 Hom.: 5704

Bravo AF: 0.261

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.77
Dann	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs578784; hg19: chr11-112000303;