rs1416483

chr6-150407426-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;