11-112882384-C-A

Position:

• chr11-112882384-C-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 0.191 in 152,058 control chromosomes in the GnomAD database, including 3,924 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 0.19 (3924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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: 0.191 AC: 29023 AN: 151940 Hom.: 3921 Cov.: 32

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.191 AC: 29022 AN: 152058 Hom.: 3924 Cov.: 32 AF XY: 0.202 AC XY: 14987 AN XY: 74334

Gnomad4 AFR AF: 0.0542

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.202

Alfa AF: 0.201 Hom.: 3458

Bravo AF: 0.190

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4937786; hg19: chr11-112753107;