chr4-25941129-A-G

Variant names:

• chr4-25941129-A-G
• rs7654585

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 0.594 in 152,044 control chromosomes in the GnomAD database, including 26,862 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 0.59 (26862 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 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: 0.594 AC: 90218 AN: 151926 Hom.: 26843 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.594 AC: 90283 AN: 152044 Hom.: 26862 Cov.: 32 AF XY: 0.592 AC XY: 43969 AN XY: 74330

African (AFR) AF: 0.598 AC: 24800 AN: 41454

American (AMR) AF: 0.601 AC: 9184 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1979 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2570 AN: 5174

South Asian (SAS) AF: 0.463 AC: 2233 AN: 4818

European-Finnish (FIN) AF: 0.611 AC: 6461 AN: 10580

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41150 AN: 67962

Other (OTH) AF: 0.579 AC: 1221 AN: 2110

Alfa AF: 0.596 Hom.: 87023

Bravo AF: 0.596

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7654585; hg19: chr4-25942751;