rs17084870

chr6-154001443-G-T

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 0.2 in 152,088 control chromosomes in the GnomAD database, including 3,311 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 (3311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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: 0.200 AC: 30460 AN: 151970 Hom.: 3314 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.200 AC: 30467 AN: 152088 Hom.: 3311 Cov.: 32 AF XY: 0.210 AC XY: 15647 AN XY: 74346

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.200

Alfa AF: 0.189 Hom.: 482

Bravo AF: 0.195

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.088
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17084870; hg19: chr6-154322578;