rs17690171

Variant names:

• chr17-66206739-T-C
• rs17690171

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 0.18 in 150,942 control chromosomes in the GnomAD database, including 2,654 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 0.18 (2654 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 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: 0.180 AC: 27102 AN: 150824 Hom.: 2653 Cov.: 30

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.180 AC: 27103 AN: 150942 Hom.: 2654 Cov.: 30 AF XY: 0.180 AC XY: 13228 AN XY: 73624

African (AFR) AF: 0.137 AC: 5658 AN: 41168

American (AMR) AF: 0.171 AC: 2581 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1057 AN: 3452

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5192

South Asian (SAS) AF: 0.106 AC: 507 AN: 4786

European-Finnish (FIN) AF: 0.265 AC: 2752 AN: 10394

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13939 AN: 67610

Other (OTH) AF: 0.193 AC: 400 AN: 2076

Alfa AF: 0.205 Hom.: 4716

Bravo AF: 0.174

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.9
DANN	Benign	0.62
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs17690171; hg19: chr17-64202857;