rs17684894

Variant names:

• chr8-137523554-T-C
• rs17684894

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 0.155 in 152,074 control chromosomes in the GnomAD database, including 1,885 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 0.15 (1885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23520 AN: 151956 Hom.: 1886 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.155 AC: 23519 AN: 152074 Hom.: 1885 Cov.: 32 AF XY: 0.155 AC XY: 11500 AN XY: 74352

African (AFR) AF: 0.106 AC: 4419 AN: 41514

American (AMR) AF: 0.169 AC: 2587 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5158

South Asian (SAS) AF: 0.134 AC: 646 AN: 4810

European-Finnish (FIN) AF: 0.174 AC: 1843 AN: 10578

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11762 AN: 67962

Other (OTH) AF: 0.158 AC: 335 AN: 2114

Alfa AF: 0.169 Hom.: 519

Bravo AF: 0.154

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.55
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs17684894; hg19: chr8-138535797;