2-90203210-A-T

Position:

• chr2-90203210-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0254 in 150,922 control chromosomes in the GnomAD database, including 200 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 0.025 (200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0254 (3834/150922) while in subpopulation NFE AF= 0.0346 (2345/67754). AF 95% confidence interval is 0.0334. There are 200 homozygotes in gnomad4. There are 1764 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 200 gene

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: 0.0255 AC: 3838 AN: 150804 Hom.: 200 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0196

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0254 AC: 3834 AN: 150922 Hom.: 200 Cov.: 32 AF XY: 0.0239 AC XY: 1764 AN XY: 73698

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0243

Gnomad4 ASJ AF: 0.0626

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.0196

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0111 Hom.: 10

Bravo AF: 0.0257

Asia WGS AF: 0.00405 AC: 14 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs842160; hg19: chr2-90242076;