2-151290158-G-T

Variant names:

• chr2-151290158-G-T
• rs2278089

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 0.686 in 152,014 control chromosomes in the GnomAD database, including 36,805 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 0.69 (36805 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104160 AN: 151892 Hom.: 36735 Cov.: 33

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.686 AC: 104285 AN: 152012 Hom.: 36805 Cov.: 33 AF XY: 0.686 AC XY: 50963 AN XY: 74270

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.632

Alfa AF: 0.605 Hom.: 38285

Bravo AF: 0.701

Asia WGS AF: 0.587 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.3
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278089; hg19: chr2-152146672;