2-133887223-T-C

Variant names:

• chr2-133887223-T-C
• rs7582472

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 0.21 in 152,170 control chromosomes in the GnomAD database, including 3,386 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 0.21 (3386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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: 0.210 AC: 31897 AN: 152052 Hom.: 3385 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.210 AC: 31925 AN: 152170 Hom.: 3386 Cov.: 32 AF XY: 0.214 AC XY: 15909 AN XY: 74392

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.222

Alfa AF: 0.212 Hom.: 2256

Bravo AF: 0.212

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7582472; hg19: chr2-134644794;