2-216104125-G-C

Position:

• chr2-216104125-G-C

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 0.888 in 152,320 control chromosomes in the GnomAD database, including 60,427 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 0.89 (60427 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 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: 0.888 AC: 135119 AN: 152202 Hom.: 60370 Cov.: 34

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.888 AC: 135234 AN: 152320 Hom.: 60427 Cov.: 34 AF XY: 0.886 AC XY: 65981 AN XY: 74476

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.862

Alfa AF: 0.868 Hom.: 2835

Bravo AF: 0.893

Asia WGS AF: 0.757 AC: 2631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.076
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs828918; hg19: chr2-216968848;