2-146027835-A-T

Variant names:

• chr2-146027835-A-T
• rs10928276

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 0.338 in 152,120 control chromosomes in the GnomAD database, including 10,737 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 0.34 (10737 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

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 (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.338 AC: 51410 AN: 152002 Hom.: 10741 Cov.: 31

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.338 AC: 51405 AN: 152120 Hom.: 10737 Cov.: 31 AF XY: 0.339 AC XY: 25203 AN XY: 74356

Gnomad4 AFR AF: 0.0884

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.356

Alfa AF: 0.374 Hom.: 1453

Bravo AF: 0.337

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.54
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10928276; hg19: chr2-146785403;