2-146027835-A-T

Variant names:

• chr2-146027835-A-T
• rs10928276

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0884 AC: 3672 AN: 41544

American (AMR) AF: 0.408 AC: 6228 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3360 AN: 5156

South Asian (SAS) AF: 0.345 AC: 1663 AN: 4822

European-Finnish (FIN) AF: 0.361 AC: 3820 AN: 10568

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29966 AN: 67970

Other (OTH) AF: 0.356 AC: 753 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.54
DANN	Benign	0.30
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10928276; hg19: chr2-146785403;