2-146028495-A-G

Position:

• chr2-146028495-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 (1318 hom., cov: 7)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.241 AC: 11032 AN: 45782 Hom.: 1316 Cov.: 7

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.241 AC: 11027 AN: 45810 Hom.: 1318 Cov.: 7 AF XY: 0.244 AC XY: 5315 AN XY: 21754

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.301

Alfa AF: 0.340 Hom.: 711

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11681122; hg19: chr2-146786063;