2-53334437-T-C

Variant names:

• chr2-53334437-T-C
• rs12328023

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 0.62 in 151,992 control chromosomes in the GnomAD database, including 30,619 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 0.62 (30619 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.620 AC: 94089 AN: 151872 Hom.: 30574 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.620 AC: 94186 AN: 151992 Hom.: 30619 Cov.: 31 AF XY: 0.623 AC XY: 46273 AN XY: 74284

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.583

Alfa AF: 0.525 Hom.: 28321

Bravo AF: 0.629

Asia WGS AF: 0.683 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12328023; hg19: chr2-53561575;