rs17083553

Variant names:

• chr6-121412523-G-T
• rs17083553

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 0.204 in 152,030 control chromosomes in the GnomAD database, including 3,349 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 0.20 (3349 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 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: 0.204 AC: 30945 AN: 151912 Hom.: 3341 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.204 AC: 30985 AN: 152030 Hom.: 3349 Cov.: 32 AF XY: 0.202 AC XY: 14995 AN XY: 74324

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.186

Alfa AF: 0.187 Hom.: 3039

Bravo AF: 0.217

Asia WGS AF: 0.191 AC: 663 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17083553; hg19: chr6-121733669; COSMIC: COSV60276857;