7-125566913-C-T

Variant names:

• chr7-125566913-C-T
• rs702458

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 151,810 control chromosomes in the GnomAD database, including 647 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 (647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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: 8349 AN: 151694 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.000759

Gnomad MID AF: 0.0130

Gnomad NFE AF: 0.00655

Gnomad OTH AF: 0.0432

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

GnomAD4 genome AF: 0.0552 AC: 8378 AN: 151810 Hom.: 647 Cov.: 32 AF XY: 0.0536 AC XY: 3975 AN XY: 74190

African (AFR) AF: 0.170 AC: 7040 AN: 41442

American (AMR) AF: 0.0340 AC: 519 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3468

East Asian (EAS) AF: 0.0444 AC: 229 AN: 5160

South Asian (SAS) AF: 0.00270 AC: 13 AN: 4822

European-Finnish (FIN) AF: 0.000759 AC: 8 AN: 10544

Middle Eastern (MID) AF: 0.0140 AC: 4 AN: 286

European-Non Finnish (NFE) AF: 0.00655 AC: 444 AN: 67808

Other (OTH) AF: 0.0433 AC: 91 AN: 2102

Alfa AF: 0.00944 Hom.: 15

Bravo AF: 0.0633

Asia WGS AF: 0.0250 AC: 88 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.24
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs702458; hg19: chr7-125206967;