7-25568789-G-A

Variant names:

• chr7-25568789-G-A
• rs17151904

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 0.24 in 152,188 control chromosomes in the GnomAD database, including 4,788 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 0.24 (4788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.240 AC: 36444 AN: 152070 Hom.: 4783 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.240 AC: 36497 AN: 152188 Hom.: 4788 Cov.: 32 AF XY: 0.239 AC XY: 17773 AN XY: 74404

African (AFR) AF: 0.287 AC: 11920 AN: 41504

American (AMR) AF: 0.210 AC: 3212 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2522 AN: 5176

South Asian (SAS) AF: 0.286 AC: 1383 AN: 4828

European-Finnish (FIN) AF: 0.168 AC: 1782 AN: 10596

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14222 AN: 68004

Other (OTH) AF: 0.228 AC: 483 AN: 2114

Alfa AF: 0.212 Hom.: 4716

Bravo AF: 0.244

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.53
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17151904; hg19: chr7-25608409;