4-45523162-G-T

Variant names:

• chr4-45523162-G-T
• rs9291270

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 0.0552 in 152,094 control chromosomes in the GnomAD database, including 320 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 0.055 (320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0867 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: 0.0550 AC: 8361 AN: 151976 Hom.: 312 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0552 AC: 8389 AN: 152094 Hom.: 320 Cov.: 32 AF XY: 0.0548 AC XY: 4071 AN XY: 74354

African (AFR) AF: 0.0891 AC: 3689 AN: 41420

American (AMR) AF: 0.0522 AC: 798 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3468

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5186

South Asian (SAS) AF: 0.0577 AC: 278 AN: 4822

European-Finnish (FIN) AF: 0.0437 AC: 463 AN: 10586

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0415 AC: 2821 AN: 68006

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0392 Hom.: 62

Bravo AF: 0.0575

Asia WGS AF: 0.0370 AC: 128 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.47
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs9291270; hg19: chr4-45525179;