rs17309585

Variant names:

• chr8-107854594-C-T
• rs17309585

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.266 in 151,958 control chromosomes in the GnomAD database, including 6,671 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 0.27 (6671 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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: 0.266 AC: 40378 AN: 151840 Hom.: 6671 Cov.: 31

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.266 AC: 40388 AN: 151958 Hom.: 6671 Cov.: 31 AF XY: 0.264 AC XY: 19573 AN XY: 74244

African (AFR) AF: 0.0981 AC: 4067 AN: 41476

American (AMR) AF: 0.237 AC: 3615 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3468

East Asian (EAS) AF: 0.0256 AC: 132 AN: 5164

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4812

European-Finnish (FIN) AF: 0.375 AC: 3952 AN: 10546

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.368 AC: 25018 AN: 67932

Other (OTH) AF: 0.290 AC: 611 AN: 2108

Alfa AF: 0.337 Hom.: 39480

Bravo AF: 0.250

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	15
DANN	Benign	0.60
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs17309585; hg19: chr8-108866822;