rs1416483

Variant names:

• chr6-150407426-G-C
• rs1416483

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 0.223 in 152,120 control chromosomes in the GnomAD database, including 4,355 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 0.22 (4355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 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: 0.223 AC: 33826 AN: 152002 Hom.: 4352 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.223 AC: 33848 AN: 152120 Hom.: 4355 Cov.: 32 AF XY: 0.227 AC XY: 16874 AN XY: 74376

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.235

Alfa AF: 0.204 Hom.: 425

Bravo AF: 0.231

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1416483; hg19: chr6-150728562;