11-2027906-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.33 (1139 hom., cov: 4)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.00 AC: 5212 AN: 15730 Hom.: 1138 Cov.: 4 FAILED QC

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.390

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.331 AC: 5214 AN: 15766 Hom.: 1139 Cov.: 4 AF XY: 0.321 AC XY: 2259 AN XY: 7040

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.399

Alfa AF: 0.171 Hom.: 362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	6.2
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7106395; hg19: chr11-2049136;