chr4-18023406-G-A

Variant names:

• chr4-18023406-G-A
• rs7668417

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 0.238 in 152,174 control chromosomes in the GnomAD database, including 5,485 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 0.24 (5485 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.237 AC: 36078 AN: 152056 Hom.: 5453 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.238 AC: 36151 AN: 152174 Hom.: 5485 Cov.: 33 AF XY: 0.233 AC XY: 17355 AN XY: 74404

African (AFR) AF: 0.426 AC: 17685 AN: 41474

American (AMR) AF: 0.196 AC: 2991 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.134 AC: 697 AN: 5184

South Asian (SAS) AF: 0.277 AC: 1339 AN: 4832

European-Finnish (FIN) AF: 0.0915 AC: 970 AN: 10606

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10715 AN: 68008

Other (OTH) AF: 0.234 AC: 494 AN: 2114

Alfa AF: 0.240 Hom.: 2100

Bravo AF: 0.251

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs7668417; hg19: chr4-18025029;