7-25911725-A-G

Variant names:

• chr7-25911725-A-G
• rs1966841

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 0.544 in 152,000 control chromosomes in the GnomAD database, including 24,002 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 0.54 (24002 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.544 AC: 82681 AN: 151882 Hom.: 24000 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.544 AC: 82721 AN: 152000 Hom.: 24002 Cov.: 31 AF XY: 0.549 AC XY: 40750 AN XY: 74278

African (AFR) AF: 0.362 AC: 15020 AN: 41454

American (AMR) AF: 0.556 AC: 8483 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2423 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4839 AN: 5184

South Asian (SAS) AF: 0.737 AC: 3549 AN: 4814

European-Finnish (FIN) AF: 0.600 AC: 6307 AN: 10504

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40125 AN: 67990

Other (OTH) AF: 0.582 AC: 1231 AN: 2114

Alfa AF: 0.580 Hom.: 81708

Bravo AF: 0.535

Asia WGS AF: 0.795 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Benign	0.92
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1966841; hg19: chr7-25951345;