5-4966782-A-G

Variant names:

• chr5-4966782-A-G
• rs2115289

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.391

Alfa AF: 0.381 Hom.: 2409

Bravo AF: 0.454

Asia WGS AF: 0.454 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2115289; hg19: chr5-4966895;