rs1828416

Variant names:

• chr4-66558092-C-T
• rs1828416

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 0.17 in 152,058 control chromosomes in the GnomAD database, including 4,077 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 0.17 (4077 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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: 0.169 AC: 25722 AN: 151940 Hom.: 4055 Cov.: 33

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.170 AC: 25791 AN: 152058 Hom.: 4077 Cov.: 33 AF XY: 0.167 AC XY: 12409 AN XY: 74318

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0931 Hom.: 722

Bravo AF: 0.179

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1828416; hg19: chr4-67423810;