rs12655917

Variant names:

• chr5-77996116-G-A
• rs12655917

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0449 in 152,246 control chromosomes in the GnomAD database, including 289 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 0.045 (289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.27

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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: 0.0449 AC: 6836 AN: 152128 Hom.: 289 Cov.: 33

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0449 AC: 6839 AN: 152246 Hom.: 289 Cov.: 33 AF XY: 0.0463 AC XY: 3447 AN XY: 74444

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0662

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0414

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0484 Hom.: 289

Bravo AF: 0.0510

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	20
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12655917; hg19: chr5-77291940;