2-89228414-A-G

Position:

• chr2-89228414-A-G

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 0.079 (871 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.12).

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: 0.00 AC: 8460 AN: 106500 Hom.: 867 Cov.: 26 FAILED QC

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0130

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.0503

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.0727

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: 0.0794 AC: 8463 AN: 106534 Hom.: 871 Cov.: 26 AF XY: 0.0724 AC XY: 3770 AN XY: 52100

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0503

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.0896

Gnomad4 FIN AF: 0.0218

Gnomad4 NFE AF: 0.0407

Gnomad4 OTH AF: 0.0717

Alfa AF: 0.0156 Hom.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.087
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs375385; hg19: chr2-89527895; COSMIC: COSV67689174;