4-57902288-C-T

Variant names:

• chr4-57902288-C-T
• rs10517418

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 0.454 in 151,840 control chromosomes in the GnomAD database, including 16,185 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 0.45 (16185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.454 AC: 68857 AN: 151722 Hom.: 16158 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.454 AC: 68939 AN: 151840 Hom.: 16185 Cov.: 32 AF XY: 0.451 AC XY: 33496 AN XY: 74206

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.477

Alfa AF: 0.415 Hom.: 26855

Bravo AF: 0.474

Asia WGS AF: 0.422 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517418; hg19: chr4-58768454;