rs6477450

Variant names:

• chr9-105677156-A-T
• rs6477450

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 0.524 in 152,088 control chromosomes in the GnomAD database, including 23,803 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 0.52 (23803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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: 0.523 AC: 79524 AN: 151970 Hom.: 23756 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.524 AC: 79625 AN: 152088 Hom.: 23803 Cov.: 32 AF XY: 0.521 AC XY: 38716 AN XY: 74348

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.538

Alfa AF: 0.458 Hom.: 2311

Bravo AF: 0.551

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6477450; hg19: chr9-108439437;