chr2-133680388-C-A

Variant names:

• chr2-133680388-C-A
• rs1901440

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 0.589 in 152,092 control chromosomes in the GnomAD database, including 27,789 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 0.59 (27789 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 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: 0.589 AC: 89573 AN: 151974 Hom.: 27763 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.589 AC: 89651 AN: 152092 Hom.: 27789 Cov.: 33 AF XY: 0.596 AC XY: 44308 AN XY: 74366

African (AFR) AF: 0.391 AC: 16209 AN: 41476

American (AMR) AF: 0.617 AC: 9432 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2334 AN: 3472

East Asian (EAS) AF: 0.790 AC: 4087 AN: 5174

South Asian (SAS) AF: 0.671 AC: 3232 AN: 4820

European-Finnish (FIN) AF: 0.721 AC: 7617 AN: 10568

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.658 AC: 44753 AN: 67980

Other (OTH) AF: 0.614 AC: 1297 AN: 2112

Alfa AF: 0.634 Hom.: 76570

Bravo AF: 0.573

Asia WGS AF: 0.718 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1901440; hg19: chr2-134437959;