rs17085569

Variant names:

• chr6-154617088-G-A
• rs17085569

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.276 in 151,912 control chromosomes in the GnomAD database, including 6,106 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 0.28 (6106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.276 AC: 41918 AN: 151800 Hom.: 6092 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.276 AC: 41963 AN: 151912 Hom.: 6106 Cov.: 32 AF XY: 0.276 AC XY: 20520 AN XY: 74240

African (AFR) AF: 0.359 AC: 14878 AN: 41408

American (AMR) AF: 0.262 AC: 4003 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1005 AN: 5170

South Asian (SAS) AF: 0.143 AC: 686 AN: 4808

European-Finnish (FIN) AF: 0.289 AC: 3030 AN: 10492

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16174 AN: 67968

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.264 Hom.: 987

Bravo AF: 0.281

Asia WGS AF: 0.189 AC: 657 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	3.7
DANN	Benign	0.23
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs17085569; hg19: chr6-154938222;