rs17069122

chr6-108002555-G-A

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 0.0216 in 152,278 control chromosomes in the GnomAD database, including 104 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 0.022 (104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 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: 0.0216 AC: 3284 AN: 152162 Hom.: 104 Cov.: 32

Gnomad AFR AF: 0.00401

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0142

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.00659

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0216 AC: 3282 AN: 152278 Hom.: 104 Cov.: 32 AF XY: 0.0237 AC XY: 1761 AN XY: 74458

Gnomad4 AFR AF: 0.00399

Gnomad4 AMR AF: 0.0142

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.00659

Gnomad4 NFE AF: 0.0187

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0213 Hom.: 94

Bravo AF: 0.0206

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.7
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17069122; hg19: chr6-108323759;