4-4882009-T-G

Variant names:

• chr4-4882009-T-G
• rs6832405

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 0.746 in 152,158 control chromosomes in the GnomAD database, including 42,917 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 0.75 (42917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.883 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: 0.746 AC: 113401 AN: 152040 Hom.: 42863 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.746 AC: 113508 AN: 152158 Hom.: 42917 Cov.: 32 AF XY: 0.752 AC XY: 55981 AN XY: 74400

African (AFR) AF: 0.865 AC: 35930 AN: 41526

American (AMR) AF: 0.723 AC: 11056 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2478 AN: 3466

East Asian (EAS) AF: 0.905 AC: 4702 AN: 5196

South Asian (SAS) AF: 0.788 AC: 3788 AN: 4810

European-Finnish (FIN) AF: 0.761 AC: 8057 AN: 10586

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45287 AN: 67964

Other (OTH) AF: 0.721 AC: 1522 AN: 2112

Alfa AF: 0.704 Hom.: 55665

Bravo AF: 0.745

Asia WGS AF: 0.834 AC: 2900 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	4.0
DANN	Benign	0.69
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6832405; hg19: chr4-4883736;