2-21050706-T-G

Position:

• chr2-21050706-T-G

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 0.0363 in 152,330 control chromosomes in the GnomAD database, including 230 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 0.036 (230 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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 (EAS) allele frequency at 95% confidence interval = 0.143 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: 0.0363 AC: 5521 AN: 152212 Hom.: 230 Cov.: 33

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.00537

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.00494

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0363 AC: 5528 AN: 152330 Hom.: 230 Cov.: 33 AF XY: 0.0364 AC XY: 2711 AN XY: 74500

Gnomad4 AFR AF: 0.0914

Gnomad4 AMR AF: 0.0218

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.00537

Gnomad4 NFE AF: 0.00494

Gnomad4 OTH AF: 0.0392

Alfa AF: 0.0281 Hom.: 24

Bravo AF: 0.0415

Asia WGS AF: 0.0660 AC: 228 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	0.99
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11893021; hg19: chr2-21273578;