chr2-146120874-A-G

Position:

• chr2-146120874-A-G

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 0.936 in 152,262 control chromosomes in the GnomAD database, including 66,929 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 0.94 (66929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

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 (NFE) allele frequency at 95% confidence interval = 0.976 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: 0.936 AC: 142368 AN: 152144 Hom.: 66897 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.936 AC: 142457 AN: 152262 Hom.: 66929 Cov.: 32 AF XY: 0.934 AC XY: 69541 AN XY: 74452

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.945

Alfa AF: 0.957 Hom.: 12452

Bravo AF: 0.926

Asia WGS AF: 0.919 AC: 3198 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	2.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs222827; hg19: chr2-146878442;