rs9282978

chr5-56689478-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 0.136 in 152,108 control chromosomes in the GnomAD database, including 2,604 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 0.14 (2604 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.136 AC: 20620 AN: 151990 Hom.: 2590 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.136 AC: 20685 AN: 152108 Hom.: 2604 Cov.: 31 AF XY: 0.134 AC XY: 9978 AN XY: 74384

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0474

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0610 Hom.: 773

Bravo AF: 0.144

Asia WGS AF: 0.219 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.4
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9282978; hg19: chr5-55985305;