5-18483542-C-T

Variant names:

• chr5-18483542-C-T
• rs4866334

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 0.927 in 151,912 control chromosomes in the GnomAD database, including 65,294 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 0.93 (65294 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140681 AN: 151794 Hom.: 65245 Cov.: 31

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.927 AC: 140790 AN: 151912 Hom.: 65294 Cov.: 31 AF XY: 0.927 AC XY: 68835 AN XY: 74248

African (AFR) AF: 0.924 AC: 38300 AN: 41454

American (AMR) AF: 0.946 AC: 14387 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3297 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4775 AN: 5148

South Asian (SAS) AF: 0.973 AC: 4698 AN: 4826

European-Finnish (FIN) AF: 0.885 AC: 9360 AN: 10578

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 62925 AN: 67916

Other (OTH) AF: 0.929 AC: 1962 AN: 2112

Alfa AF: 0.928 Hom.: 90171

Bravo AF: 0.930

Asia WGS AF: 0.954 AC: 3318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4866334; hg19: chr5-18483651;