2-146178926-C-T

Variant names:

• chr2-146178926-C-T
• rs10928280

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 152,062 control chromosomes in the GnomAD database, including 67,923 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 (67923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 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: 0.943 AC: 143324 AN: 151944 Hom.: 67895 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.943 AC: 143409 AN: 152062 Hom.: 67923 Cov.: 32 AF XY: 0.941 AC XY: 69948 AN XY: 74344

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.948

Alfa AF: 0.968 Hom.: 8869

Bravo AF: 0.932

Asia WGS AF: 0.919 AC: 3165 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10928280; hg19: chr2-146936494;