17-66920916-A-T

Variant names:

• chr17-66920916-A-T
• rs17645023

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 0.225 in 152,174 control chromosomes in the GnomAD database, including 3,858 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 0.22 (3858 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 14 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 (SAS) allele frequency at 95% confidence interval = 0.285 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: 0.224 AC: 34135 AN: 152056 Hom.: 3855 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.225 AC: 34167 AN: 152174 Hom.: 3858 Cov.: 32 AF XY: 0.224 AC XY: 16684 AN XY: 74382

African (AFR) AF: 0.212 AC: 8799 AN: 41510

American (AMR) AF: 0.258 AC: 3950 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 917 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1361 AN: 5172

South Asian (SAS) AF: 0.298 AC: 1434 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1700 AN: 10590

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15325 AN: 68002

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.227 Hom.: 2235

Bravo AF: 0.230

Asia WGS AF: 0.295 AC: 1028 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	0.022
DANN	Benign	0.35
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17645023; hg19: chr17-64917033;