4-4882009-T-G

Position:

• chr4-4882009-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;