chr4-154594264-C-G

Variant names:

• chr4-154594264-C-G
• rs7659613

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 0.563 in 151,936 control chromosomes in the GnomAD database, including 24,473 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 0.56 (24473 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 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: 0.563 AC: 85539 AN: 151818 Hom.: 24455 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.563 AC: 85588 AN: 151936 Hom.: 24473 Cov.: 31 AF XY: 0.562 AC XY: 41710 AN XY: 74252

African (AFR) AF: 0.464 AC: 19206 AN: 41424

American (AMR) AF: 0.619 AC: 9450 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2011 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2584 AN: 5162

South Asian (SAS) AF: 0.552 AC: 2661 AN: 4818

European-Finnish (FIN) AF: 0.540 AC: 5688 AN: 10538

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41942 AN: 67948

Other (OTH) AF: 0.605 AC: 1279 AN: 2114

Alfa AF: 0.484 Hom.: 1482

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.44
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7659613; hg19: chr4-155515416;