2-53408128-C-T

Variant names:

• chr2-53408128-C-T
• rs7582207

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.26 (4371 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.265 AC: 29507 AN: 111454 Hom.: 4367 Cov.: 19

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.265 AC: 29546 AN: 111546 Hom.: 4371 Cov.: 19 AF XY: 0.278 AC XY: 14238 AN XY: 51178

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.277

Alfa AF: 0.135 Hom.: 1467

Bravo AF: 0.240

Asia WGS AF: 0.308 AC: 1070 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.54
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7582207; hg19: chr2-53635266;