2-53324462-C-T

Variant names:

• chr2-53324462-C-T
• rs1011572

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 0.42 in 151,996 control chromosomes in the GnomAD database, including 13,688 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 0.42 (13688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• 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 (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63817 AN: 151876 Hom.: 13665 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.420 AC: 63888 AN: 151996 Hom.: 13688 Cov.: 32 AF XY: 0.422 AC XY: 31370 AN XY: 74250

African (AFR) AF: 0.466 AC: 19336 AN: 41470

American (AMR) AF: 0.497 AC: 7588 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1951 AN: 5172

South Asian (SAS) AF: 0.425 AC: 2044 AN: 4814

European-Finnish (FIN) AF: 0.465 AC: 4896 AN: 10524

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25650 AN: 67964

Other (OTH) AF: 0.392 AC: 827 AN: 2108

Alfa AF: 0.392 Hom.: 31513

Bravo AF: 0.423

Asia WGS AF: 0.402 AC: 1396 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	2.4
DANN	Benign	0.60
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs1011572; hg19: chr2-53551600;