2-20981153-G-T

Position:

• chr2-20981153-G-T

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 0.242 in 152,094 control chromosomes in the GnomAD database, including 5,507 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 0.24 (5507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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: 0.242 AC: 36757 AN: 151974 Hom.: 5508 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.242 AC: 36752 AN: 152094 Hom.: 5507 Cov.: 32 AF XY: 0.249 AC XY: 18525 AN XY: 74354

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.246

Alfa AF: 0.263 Hom.: 7866

Bravo AF: 0.233

Asia WGS AF: 0.586 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6544366; hg19: chr2-21204025;