2-55278320-C-T

Variant names:

• chr2-55278320-C-T
• rs1437396

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 0.326 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.326 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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.337

Alfa AF: 0.155 Hom.: 437

Bravo AF: 0.193

Asia WGS AF: 0.302 AC: 1047 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437396; hg19: chr2-55505456;