rs1883339

Variant names:

• chr6-132279845-G-A
• rs1883339

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 0.206 in 152,140 control chromosomes in the GnomAD database, including 7,571 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 (7571 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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: 0.206 AC: 31288 AN: 152020 Hom.: 7534 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.206 AC: 31374 AN: 152140 Hom.: 7571 Cov.: 32 AF XY: 0.202 AC XY: 15043 AN XY: 74380

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0626

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.177

Alfa AF: 0.158 Hom.: 1310

Bravo AF: 0.228

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883339; hg19: chr6-132600984;