rs17489282

Variant names:

• chr8-19995007-C-T
• rs17489282

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 0.255 in 152,146 control chromosomes in the GnomAD database, including 4,999 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 0.25 (4999 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38782 AN: 152026 Hom.: 4999 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.255 AC: 38795 AN: 152146 Hom.: 4999 Cov.: 33 AF XY: 0.254 AC XY: 18920 AN XY: 74370

African (AFR) AF: 0.239 AC: 9919 AN: 41492

American (AMR) AF: 0.240 AC: 3670 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1068 AN: 5182

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4826

European-Finnish (FIN) AF: 0.244 AC: 2582 AN: 10568

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18190 AN: 68000

Other (OTH) AF: 0.252 AC: 532 AN: 2114

Alfa AF: 0.250 Hom.: 1379

Bravo AF: 0.252

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17489282;

hg19: chr8-19852518;