17-82077020-C-T

Variant names:

• chr17-82077020-C-T
• rs12949488

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 0.273 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.377 AC: 15652 AN: 41508

American (AMR) AF: 0.400 AC: 6116 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 848 AN: 3468

East Asian (EAS) AF: 0.101 AC: 524 AN: 5190

South Asian (SAS) AF: 0.157 AC: 757 AN: 4828

European-Finnish (FIN) AF: 0.256 AC: 2710 AN: 10594

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14073 AN: 67998

Other (OTH) AF: 0.280 AC: 590 AN: 2110

Alfa AF: 0.273 Hom.: 4580

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12949488; hg19: chr17-80034896;