chr17-82076567-C-T

Variant names:

• chr17-82076567-C-T
• rs8066956

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 0.174 in 152,202 control chromosomes in the GnomAD database, including 2,693 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 0.17 (2693 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26450 AN: 152084 Hom.: 2693 Cov.: 33

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.174 AC: 26444 AN: 152202 Hom.: 2693 Cov.: 33 AF XY: 0.173 AC XY: 12877 AN XY: 74392

African (AFR) AF: 0.0690 AC: 2865 AN: 41550

American (AMR) AF: 0.175 AC: 2673 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1033 AN: 5182

South Asian (SAS) AF: 0.235 AC: 1131 AN: 4820

European-Finnish (FIN) AF: 0.168 AC: 1785 AN: 10598

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15233 AN: 67982

Other (OTH) AF: 0.209 AC: 440 AN: 2106

Alfa AF: 0.213 Hom.: 5507

Bravo AF: 0.172

Asia WGS AF: 0.232 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.3
DANN	Benign	0.90
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs8066956; hg19: chr17-80034443;