17-66206739-T-C

Position:

• chr17-66206739-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.193

Alfa AF: 0.208 Hom.: 3904

Bravo AF: 0.174

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17690171; hg19: chr17-64202857;