rs555817

Variant names:

• chr5-132122104-C-G
• rs555817

Your query was ambiguous. Multiple possible variants found:

• chr5-132122104-C-G
• chr5-132122104-C-T

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 0.291 in 151,732 control chromosomes in the GnomAD database, including 7,884 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 0.29 (7884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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: 0.290 AC: 44028 AN: 151614 Hom.: 7853 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.291 AC: 44119 AN: 151732 Hom.: 7884 Cov.: 32 AF XY: 0.289 AC XY: 21432 AN XY: 74252

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.246

Alfa AF: 0.120 Hom.: 183

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.74
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs555817; hg19: chr5-131457797;