2-55278320-C-T

Variant names:

• chr2-55278320-C-T
• rs1437396

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 0.326 in 90,992 control chromosomes in the GnomAD database, including 3,392 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 0.33 (3392 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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: 0.326 AC: 29653 AN: 90922 Hom.: 3389 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.326 AC: 29672 AN: 90992 Hom.: 3392 Cov.: 33 AF XY: 0.330 AC XY: 14407 AN XY: 43714

African (AFR) AF: 0.226 AC: 4159 AN: 18386

American (AMR) AF: 0.343 AC: 2778 AN: 8096

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 504 AN: 2386

East Asian (EAS) AF: 0.551 AC: 2380 AN: 4322

South Asian (SAS) AF: 0.320 AC: 954 AN: 2978

European-Finnish (FIN) AF: 0.303 AC: 1717 AN: 5670

Middle Eastern (MID) AF: 0.328 AC: 63 AN: 192

European-Non Finnish (NFE) AF: 0.350 AC: 16502 AN: 47110

Other (OTH) AF: 0.337 AC: 411 AN: 1220

Alfa AF: 0.154 Hom.: 496

Bravo AF: 0.193

Asia WGS AF: 0.302 AC: 1047 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.42
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1437396; hg19: chr2-55505456;