4-4882009-T-G

Variant names:

• chr4-4882009-T-G
• rs6832405

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.721

Alfa AF: 0.730 Hom.: 5627

Bravo AF: 0.745

Asia WGS AF: 0.834 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6832405; hg19: chr4-4883736;