chr4-4889421-C-T

Variant names:

• chr4-4889421-C-T
• rs6817411

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;