chr5-39694297-C-T

Variant names:

• chr5-39694297-C-T
• rs1499238

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 0.889 in 152,206 control chromosomes in the GnomAD database, including 60,760 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 0.89 (60760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 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: 0.889 AC: 135169 AN: 152086 Hom.: 60719 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.889 AC: 135265 AN: 152206 Hom.: 60760 Cov.: 32 AF XY: 0.884 AC XY: 65819 AN XY: 74430

African (AFR) AF: 0.830 AC: 34439 AN: 41498

American (AMR) AF: 0.826 AC: 12623 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3281 AN: 3472

East Asian (EAS) AF: 0.530 AC: 2739 AN: 5168

South Asian (SAS) AF: 0.897 AC: 4327 AN: 4822

European-Finnish (FIN) AF: 0.936 AC: 9932 AN: 10610

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64869 AN: 68036

Other (OTH) AF: 0.902 AC: 1907 AN: 2114

Alfa AF: 0.936 Hom.: 32731

Bravo AF: 0.875

Asia WGS AF: 0.747 AC: 2596 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.60
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs1499238; hg19: chr5-39694399;