chr5-100613278-A-T

Variant names:

• chr5-100613278-A-T
• rs383830

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 0.767 in 152,106 control chromosomes in the GnomAD database, including 45,232 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 0.77 (45232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116635 AN: 151988 Hom.: 45185 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.767 AC: 116732 AN: 152106 Hom.: 45232 Cov.: 32 AF XY: 0.768 AC XY: 57133 AN XY: 74344

African (AFR) AF: 0.649 AC: 26910 AN: 41474

American (AMR) AF: 0.861 AC: 13154 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3020 AN: 3468

East Asian (EAS) AF: 0.830 AC: 4296 AN: 5178

South Asian (SAS) AF: 0.829 AC: 4000 AN: 4828

European-Finnish (FIN) AF: 0.791 AC: 8362 AN: 10570

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54296 AN: 67990

Other (OTH) AF: 0.807 AC: 1704 AN: 2112

Alfa AF: 0.777 Hom.: 5709

Bravo AF: 0.768

Asia WGS AF: 0.834 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.59
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs383830; hg19: chr5-99948982;