4-116305153-A-G

Variant names:

• chr4-116305153-A-G
• rs6821696

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 0.812 in 152,044 control chromosomes in the GnomAD database, including 50,294 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 0.81 (50294 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123334 AN: 151926 Hom.: 50252 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.812 AC: 123437 AN: 152044 Hom.: 50294 Cov.: 31 AF XY: 0.802 AC XY: 59611 AN XY: 74300

African (AFR) AF: 0.807 AC: 33452 AN: 41474

American (AMR) AF: 0.778 AC: 11873 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3518 AN: 5146

South Asian (SAS) AF: 0.729 AC: 3515 AN: 4824

European-Finnish (FIN) AF: 0.753 AC: 7942 AN: 10554

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58045 AN: 67990

Other (OTH) AF: 0.766 AC: 1617 AN: 2112

Alfa AF: 0.834 Hom.: 165233

Bravo AF: 0.815

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.26
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6821696; hg19: chr4-117226309;