rs1477479

Positions:

• chr9-21178518-A-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 0.213 in 154,630 control chromosomes in the GnomAD database, including 3,889 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 0.21 (3843 hom., cov: 32)
  • Exomes 𝑓: 0.16 (46 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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: 0.213 AC: 32430 AN: 152040 Hom.: 3835 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.165 AC: 407 AN: 2472 Hom.: 46 AF XY: 0.162 AC XY: 220 AN XY: 1354

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.324

Gnomad4 ASJ exome AF: 0.118

Gnomad4 EAS exome AF: 0.324

Gnomad4 SAS exome AF: 0.133

Gnomad4 FIN exome AF: 0.166

Gnomad4 NFE exome AF: 0.155

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.214 AC: 32489 AN: 152158 Hom.: 3843 Cov.: 32 AF XY: 0.214 AC XY: 15940 AN XY: 74388

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.210

Alfa AF: 0.201 Hom.: 384

Bravo AF: 0.223

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1477479; hg19: chr9-21178517;