2-53408128-C-T

Variant names:

• chr2-53408128-C-T
• rs7582207

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.265 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

African (AFR) AF: 0.460 AC: 14444 AN: 31432

American (AMR) AF: 0.332 AC: 2955 AN: 8908

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 465 AN: 2976

East Asian (EAS) AF: 0.389 AC: 1522 AN: 3916

South Asian (SAS) AF: 0.302 AC: 1035 AN: 3422

European-Finnish (FIN) AF: 0.250 AC: 863 AN: 3446

Middle Eastern (MID) AF: 0.303 AC: 37 AN: 122

European-Non Finnish (NFE) AF: 0.140 AC: 7696 AN: 55104

Other (OTH) AF: 0.277 AC: 415 AN: 1500

Alfa AF: 0.140 Hom.: 1846

Bravo AF: 0.240

Asia WGS AF: 0.308 AC: 1070 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.54
DANN	Benign	0.39
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7582207; hg19: chr2-53635266;