rs17083533

Variant names:

• chr6-121409576-G-A
• rs17083533

Your query was ambiguous. Multiple possible variants found:

• chr6-121409576-G-A
• chr6-121409576-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 0.0341 in 152,234 control chromosomes in the GnomAD database, including 300 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 0.034 (300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 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: 0.0341 AC: 5191 AN: 152116 Hom.: 301 Cov.: 32

Gnomad AFR AF: 0.00705

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0331

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

GnomAD4 genome AF: 0.0341 AC: 5186 AN: 152234 Hom.: 300 Cov.: 32 AF XY: 0.0399 AC XY: 2973 AN XY: 74440

Gnomad4 AFR AF: 0.00702

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.00891

Gnomad4 FIN AF: 0.0872

Gnomad4 NFE AF: 0.0150

Gnomad4 OTH AF: 0.0337

Alfa AF: 0.00963 Hom.: 4

Bravo AF: 0.0385

Asia WGS AF: 0.0920 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17083533; hg19: chr6-121730722;