4-68672027-C-T

Variant names:

• chr4-68672027-C-T
• rs7682027

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 0.189 in 152,060 control chromosomes in the GnomAD database, including 3,322 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 0.19 (3322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28763 AN: 151944 Hom.: 3326 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.189 AC: 28749 AN: 152060 Hom.: 3322 Cov.: 32 AF XY: 0.189 AC XY: 14013 AN XY: 74312

African (AFR) AF: 0.0497 AC: 2065 AN: 41516

American (AMR) AF: 0.221 AC: 3374 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1427 AN: 5146

South Asian (SAS) AF: 0.176 AC: 849 AN: 4816

European-Finnish (FIN) AF: 0.210 AC: 2215 AN: 10564

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17213 AN: 67952

Other (OTH) AF: 0.201 AC: 425 AN: 2110

Alfa AF: 0.210 Hom.: 482

Bravo AF: 0.188

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.73
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7682027; hg19: chr4-69537745;