rs1828416

Variant names:

• chr4-66558092-C-T
• rs1828416

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.416 AC: 17251 AN: 41432

American (AMR) AF: 0.107 AC: 1639 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1234 AN: 10562

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4854 AN: 67978

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.0944 Hom.: 808

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
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs1828416; hg19: chr4-67423810;