5-68415296-A-G

Variant names:

• chr5-68415296-A-G
• rs16897810

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 0.103 in 152,216 control chromosomes in the GnomAD database, including 1,309 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 0.10 (1309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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: 0.103 AC: 15629 AN: 152098 Hom.: 1306 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0853

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

GnomAD4 genome AF: 0.103 AC: 15640 AN: 152216 Hom.: 1309 Cov.: 32 AF XY: 0.107 AC XY: 7940 AN XY: 74424

African (AFR) AF: 0.184 AC: 7651 AN: 41506

American (AMR) AF: 0.126 AC: 1929 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1667 AN: 5172

South Asian (SAS) AF: 0.0835 AC: 403 AN: 4826

European-Finnish (FIN) AF: 0.0396 AC: 420 AN: 10608

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0470 AC: 3195 AN: 68018

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0610 Hom.: 734

Bravo AF: 0.112

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.54
DANN	Benign	0.74
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs16897810; hg19: chr5-67711123;