chr2-53464911-G-C

Variant names:

• chr2-53464911-G-C
• rs903228

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 0.169 in 152,156 control chromosomes in the GnomAD database, including 3,338 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 0.17 (3338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25587 AN: 152038 Hom.: 3313 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.169 AC: 25669 AN: 152156 Hom.: 3338 Cov.: 32 AF XY: 0.166 AC XY: 12355 AN XY: 74382

African (AFR) AF: 0.356 AC: 14760 AN: 41476

American (AMR) AF: 0.197 AC: 3011 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.0907 AC: 469 AN: 5170

South Asian (SAS) AF: 0.0866 AC: 418 AN: 4828

European-Finnish (FIN) AF: 0.0466 AC: 494 AN: 10610

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0806 AC: 5483 AN: 67990

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.132 Hom.: 264

Bravo AF: 0.189

Asia WGS AF: 0.106 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.59
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs903228; hg19: chr2-53692049;