chr2-146120964-T-C

Position:

• chr2-146120964-T-C

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 0.943 in 152,248 control chromosomes in the GnomAD database, including 67,951 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 (67951 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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: 0.943 AC: 143532 AN: 152130 Hom.: 67921 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.926

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.943 AC: 143619 AN: 152248 Hom.: 67951 Cov.: 33 AF XY: 0.941 AC XY: 70087 AN XY: 74446

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.901

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: 0.949

Alfa AF: 0.956 Hom.: 10495

Bravo AF: 0.935

Asia WGS AF: 0.920 AC: 3199 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs222826; hg19: chr2-146878532;