2-154465122-G-A

Position:

• chr2-154465122-G-A

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 0.0699 in 151,820 control chromosomes in the GnomAD database, including 481 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 0.070 (481 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 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: 0.0698 AC: 10596 AN: 151702 Hom.: 480 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0555

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0699 AC: 10605 AN: 151820 Hom.: 481 Cov.: 31 AF XY: 0.0715 AC XY: 5302 AN XY: 74186

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0555

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0594

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0406

Gnomad4 OTH AF: 0.0560

Alfa AF: 0.0549 Hom.: 51

Bravo AF: 0.0724

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10187367; hg19: chr2-155321634;