chr4-4889421-C-T

Position:

• chr4-4889421-C-T

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 0.563 in 152,110 control chromosomes in the GnomAD database, including 24,903 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 (24903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85518 AN: 151992 Hom.: 24858 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.563 AC: 85617 AN: 152110 Hom.: 24903 Cov.: 33 AF XY: 0.572 AC XY: 42555 AN XY: 74356

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.541

Alfa AF: 0.489 Hom.: 31754

Bravo AF: 0.559

Asia WGS AF: 0.673 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6817411; hg19: chr4-4891148;