rs930922

Positions:

• chr5-117039777-A-G

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 0.192 in 152,182 control chromosomes in the GnomAD database, including 3,062 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 0.19 (3062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29164 AN: 152064 Hom.: 3058 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.192 AC: 29179 AN: 152182 Hom.: 3062 Cov.: 32 AF XY: 0.191 AC XY: 14221 AN XY: 74400

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.00597

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.205

Alfa AF: 0.229 Hom.: 5542

Bravo AF: 0.185

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs930922; hg19: chr5-116375473;