7-151553523-C-T

Variant names:

• chr7-151553523-C-T
• rs4725408

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 0.7 in 152,280 control chromosomes in the GnomAD database, including 38,441 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 0.70 (38441 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106529 AN: 152162 Hom.: 38406 Cov.: 36

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.700 AC: 106607 AN: 152280 Hom.: 38441 Cov.: 36 AF XY: 0.707 AC XY: 52685 AN XY: 74470

African (AFR) AF: 0.526 AC: 21848 AN: 41538

American (AMR) AF: 0.734 AC: 11240 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2731 AN: 3468

East Asian (EAS) AF: 0.985 AC: 5109 AN: 5188

South Asian (SAS) AF: 0.834 AC: 4030 AN: 4830

European-Finnish (FIN) AF: 0.792 AC: 8414 AN: 10618

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 51042 AN: 68014

Other (OTH) AF: 0.728 AC: 1538 AN: 2114

Alfa AF: 0.710 Hom.: 5027

Bravo AF: 0.688

Asia WGS AF: 0.898 AC: 3123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs4725408; hg19: chr7-151250609;