5-4966782-A-G

Variant names:

• chr5-4966782-A-G
• rs2115289

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 0.444 in 151,964 control chromosomes in the GnomAD database, including 16,568 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 0.44 (16568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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: 0.444 AC: 67353 AN: 151846 Hom.: 16532 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.444 AC: 67449 AN: 151964 Hom.: 16568 Cov.: 32 AF XY: 0.443 AC XY: 32887 AN XY: 74282

African (AFR) AF: 0.666 AC: 27571 AN: 41418

American (AMR) AF: 0.367 AC: 5608 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1001 AN: 3466

East Asian (EAS) AF: 0.443 AC: 2289 AN: 5168

South Asian (SAS) AF: 0.428 AC: 2063 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3847 AN: 10548

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24017 AN: 67962

Other (OTH) AF: 0.391 AC: 826 AN: 2112

Alfa AF: 0.388 Hom.: 2571

Bravo AF: 0.454

Asia WGS AF: 0.454 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.63
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2115289; hg19: chr5-4966895;