17-82077020-C-T

Position:

• chr17-82077020-C-T

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 0.273 in 152,188 control chromosomes in the GnomAD database, including 6,417 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 (6417 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.82077020C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41506 AN: 152070 Hom.: 6397 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.273 AC: 41576 AN: 152188 Hom.: 6417 Cov.: 33 AF XY: 0.273 AC XY: 20330 AN XY: 74388

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.280

Alfa AF: 0.245 Hom.: 2028

Bravo AF: 0.292

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.39
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12949488; hg19: chr17-80034896;