5-39863861-G-T

Variant names:

• chr5-39863861-G-T
• rs506056

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 0.776 in 151,682 control chromosomes in the GnomAD database, including 45,968 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 0.78 (45968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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: 0.776 AC: 117538 AN: 151564 Hom.: 45914 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.776 AC: 117652 AN: 151682 Hom.: 45968 Cov.: 32 AF XY: 0.778 AC XY: 57653 AN XY: 74106

African (AFR) AF: 0.870 AC: 35987 AN: 41384

American (AMR) AF: 0.764 AC: 11644 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2245 AN: 3466

East Asian (EAS) AF: 0.864 AC: 4455 AN: 5154

South Asian (SAS) AF: 0.762 AC: 3673 AN: 4822

European-Finnish (FIN) AF: 0.757 AC: 7939 AN: 10494

Middle Eastern (MID) AF: 0.741 AC: 215 AN: 290

European-Non Finnish (NFE) AF: 0.728 AC: 49368 AN: 67818

Other (OTH) AF: 0.750 AC: 1581 AN: 2108

Alfa AF: 0.716 Hom.: 2678

Bravo AF: 0.782

Asia WGS AF: 0.841 AC: 2921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.66
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs506056; hg19: chr5-39863963;