2-53334437-T-C

Variant names:

• chr2-53334437-T-C
• rs12328023

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 0.62 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.819 AC: 33987 AN: 41476

American (AMR) AF: 0.614 AC: 9369 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3466

East Asian (EAS) AF: 0.702 AC: 3615 AN: 5150

South Asian (SAS) AF: 0.645 AC: 3106 AN: 4812

European-Finnish (FIN) AF: 0.585 AC: 6180 AN: 10564

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34515 AN: 67940

Other (OTH) AF: 0.583 AC: 1232 AN: 2112

Alfa AF: 0.529 Hom.: 34271

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
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12328023; hg19: chr2-53561575; COSMIC: COSV107164812;